adding sugars for refinement in X-plor

'Dave' David Goetz spacecby at u.washington.edu
Thu Apr 30 19:26:49 EST 1998


To whom it may concern,
	We are working on a protein which has an N-linked glycosylation site.
We are having difficulty in getting X-plor to generate a proper .psf and .pdb
file for refinement when sugars are added to the input .pdb file. The following
contains the X-plor command input file used. The protein is separated into the
first 5 pdb files. File 2.pdb contains the Asn 65 which is N-linked to the first
sugar residue NAG (301). File 6.pdb and 7.pdb contain the sugar residues 301 and 
302 respectively. Below the input file, we have included the message output generated
by X-plor. It seems to read all the input pdb files correctly, but when the patch,
B1N, is run to create the bond from the protein to the sugar, something goes wrong.
Similarly, the patch to create the glycosidic linkage goes awry too. The patches
are from the distributed toph3.cho and are unmodified. Just to prove that the atoms
are indeed in the pdb files we have included the 15 atom long sugar files 6.pdb
and 7.pdb( the 15 hydrogens are missing but we gather that that is not a problem )
along with the asn from 2.pdb at the bottom of this rather long post.
We appreciate any and all help in resolving this matter.

Thanks,
spacecby at u.washington.edu



{*-------------------------------------------------------------------------*}
	Generate input file which doesn't work for sugars
{*-------------------------------------------------------------------------*}
	
 topology  @/sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro
	   @/sgi/local/xtal/xplor3.8/toppar/toph3.cho  end                    
 	   
parameter @/sgi/local/xtal/xplor3.8/toppar/protein_rep.param
	  @/sgi/local/xtal/xplor3.8/toppar/param3.cho  end

{*-------------------------------------------------------------------------*}

 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep   
   
   coordinates @1.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @1.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}

 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep   
   
   coordinates @2.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @2.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}

 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep   
   
   coordinates @3.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @3.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}

 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep   
   
   coordinates @4.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @4.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep   
   	 
   coordinates @5.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @5.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain    
   	 
   coordinates @6.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @6.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
{*-------------------------------------------------------------------------*}
 segment                                              {*Generate first bit.*}

   name="    "                              {*This name has to match the   *}
                                            {*four characters in columns 73*}
                                            {*through 76 in the coordinate *}
                                            {*file; in XPLOR this name is  *}
                                            {*referred to as SEGId.        *}

   chain   
   	 
   coordinates @7.pdb           {*interpret coordinate file to*}
   end                             {*obtain the sequence.        *}
 end
                                                 {*Sometimes different atom*}
 vector do (name="O") ( name OT1 )               {*names are used.         *}
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
                                    
   coordinates @7.pdb     {*Here we actually read the*}
                                            {*coordinates.             *}  
 
{*-------------------------------------------------------------------------*}
 
{===>}                                               {*Create S-S bridges.*}
 patch disu
   reference=1=( resid 76 )
   reference=2=( resid 175 )
 end
{===>}						     {*Create NAG ASN link.*}
 patch B1N
   reference=1=( resid 65 )
   reference=2=(resid 301 )
 end
 patch B14					     {*Create NAG NAG bond.*}
   reference=1=( resid 301 )
   reference=2=( resid 302 )
 end
{===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray }
        { crystallography or modelling.  Set the FALSE for most X-ray     }
        { crystallographic applications at resolution > 1. A              }
 evaluate ($hydrogen_flag=FALSE)
        
 if ($hydrogen_flag=TRUE) then
    flags exclude vdw elec end                {*Do QUICK hydrogen building w/o*}
                                              {*vdw and elec terms.           *}
    hbuild                                      {*This statement builds       *}
       selection=( hydrogen )                   {*missing hydrogens, which are*}
       phistep=45                               {*needed for the force field. *}
    end

    constraints fix=( not hydrogen ) end      {* Minimize hydrogen positions. *}
    flags include vdw end
    minimize powell 
       nstep=40 
    end
    constraints fix=( not all ) end 
 else
    delete selection=( hydrogen ) end
 end if

 {* Set occupancies and b-factors if necessary *}
 vector do (q=1.0 ) ( all )
 vector do (b=15.)  ( all )

 write coordinates output=model12_gen.pdb end         {*Write out coordinates.*} 
 write structure output=model12.psf end           {*Write out structure file.*}
 stop




{*-----------------------------------------------------------------------------*}
	X-plor output messages
{*-----------------------------------------------------------------------------*}
	 X-PLOR> topology  @/sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/tophcsdx.pro opened.
 RTFRDR>remarks file TOPPAR/tophcsdx_new.pro  (5/26/92) 
 RTFRDR>REMARKS TOPHCSDx.PRO: Original XPLOR toph19x.pro modified according to 
 RTFRDR>REMARKS R. A. Engh and R. Huber, Acta Cryst, Sect A, 1991) 
 RTFRDR>REMARKS with additional atom types. 
 RTFRDR>REMARKS =============================== 
 RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. 
 RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. 
 RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. 
 RTFRDR>REMARKS Default for HIStidines is the doubly protonated state 
 RTFRDR> 
 RTFRDR>! 
 RTFRDR>! Please cite the following reference when using these parameters: 
 RTFRDR>! Engh, R.A. and  Huber, R. (1991). Accurate Bond and 
 RTFRDR>!  Angle Parameters for X-ray Protein-Structure Refinement, 
 RTFRDR>!  Acta Cryst. A47, 392-400. 
 RTFRDR>! 
 RTFRDR>! 
 RTFRDR> 
 RTFRDR>set echo=false end 
 RTFRDR>set echo=true end 
 RTFRDR> 
 RTFRDR>           @/sgi/local/xtal/xplor3.8/toppar/toph3.cho  end 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph3.cho opened.
 RTFRDR>REMARKS toph3.cho {pyranose sugar toplogy for refinement} 
 RTFRDR>REMARKS FOR USE WITH PARAM3.CHO AND CSD PROTEIN PARAMETERS 
 RTFRDR>REMARKS ===================================================== 
 RTFRDR>REMARKS Bill Weis 10-July-1988 
 RTFRDR>REMARKS Also see PARAM1.CHO for parameters. 
 RTFRDR>REMARKS Charges taken from John Brady's glucose topology file for ring, 
 RTFRDR>REMARKS   others from protein parameter file. 
 RTFRDR>REMARKS Idealized values for impropers at ring carbons to allow simple 
 RTFRDR>REMARKS   construction of various anomers/epimers. 
 RTFRDR>REMARKS Any other hexose or link can be easily constructed by analogy to these. 
 RTFRDR> 
 RTFRDR>REMARKS Additions 6-March-1992 Bill Weis for use with PARAM2.CHO 
 RTFRDR>REMARKS New atom types CCA, CCE,  OA for the C1 & O1 positions to account 
 RTFRDR>REMARKS for different bond and angle values due to the anomeric effect. 
 RTFRDR>REMARKS More accurate equilibrium values for bond angle around this oxygen 
 RTFRDR>REMARKS in glycosidic linkages.  CCE for equatorial O1, CCA for 
 RTFRDR>REMAKRS axial O1.   For free sugar, keep OH1 as O1 atomtype; changed to OA 
 RTFRDR>REMARKS for linkages. 
 RTFRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; 
 RTFRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. 
 RTFRDR> 
 RTFRDR>REMARKS Additional CC6 atomtype for exocyclic carbon 5/11/92 
 RTFRDR> 
 RTFRDR>set echo=false end 
 RTFRDR> 
 RTFRDR>  end 
 X-PLOR>         
 X-PLOR>parameter @/sgi/local/xtal/xplor3.8/toppar/protein_rep.param 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/protein_rep.param opened.
 PARRDR>remarks file toppar/protein_rep.param 
 PARRDR>remarks Parameter file including bond and angle parameters 
 PARRDR>remarks derived from Cambridge Data Base model structures 
 PARRDR>remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991). 
 PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function. 
 PARRDR>remarks Small dihedral angle energy constants set to zero.  All other 
 PARRDR>remarks dihedral and improper energy constants set to uniform values. 
 PARRDR>remarks Water parameters are included. 
 PARRDR> 
 PARRDR>! 
 PARRDR>! References: 
 PARRDR>! Engh, R.A. and  Huber, R. (1991). Accurate Bond and 
 PARRDR>!  Angle Parameters for X-ray Protein-Structure Refinement, 
 PARRDR>!  Acta Cryst. A47, 392-400. 
 PARRDR>! 
 PARRDR>! Hendrickson W.A. and Konnert J.H. in "Computing  in 
 PARRDR>!  Crystallography"  (ed.   R.  Diamond, S. Ramaseshan 
 PARRDR>!  and K. Venkatesan) (Bangalore, Indian Institute  of 
 PARRDR>!  Science, 1980) 13.01-13.23 
 PARRDR>! 
 PARRDR> 
 PARRDR> 
 PARRDR> 
 PARRDR>set echo=off message=off end 
 PARRDR>          @/sgi/local/xtal/xplor3.8/toppar/param3.cho  end 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/param3.cho opened.
 PARRDR> 
 PARRDR>REMARKS Parameter file for pyranose sugars 
 PARRDR>REMARKS ================================== 
 PARRDR>REMARKS Bill Weis 10-July-1988 
 PARRDR>REMARKS Additions for atom type combinations not covered in PARAM19X.PRO. 
 PARRDR>REMARKS Needed additions are for ether oxygen and aliphatic carbon in all-atom 
 PARRDR>REMARKS representation used for sugars (type CC).  Ditto for type HA. 
 PARRDR>REMARKS Values from J. Brady glucose parameters unless noted. 
 PARRDR>REMARKS These should be sufficient for refinement. 
 PARRDR> 
 PARRDR>REMARKS Additions 6-March-1992 Bill Weis 
 PARRDR>REMARKS New atom types CCA, CCE,  OA for the C1 & O1 positions to account 
 PARRDR>REMARKS for different bond and angle values due to the anomeric effect. 
 PARRDR>REMARKS More accurate equilibrium values for bond angle around this oxygen 
 PARRDR>REMARKS in glycosidic linkages.  CCE for equatorial O1, CCA for 
 PARRDR>REMAKRS axial O1.   For free sugar, keep OH1 as O1 atomtype; changed to OA 
 PARRDR>REMARKS for linkages. 
 PARRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; 
 PARRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. 
 PARRDR> 
 PARRDR>REMARKS  This set has been modified to be roughly consistent with 
 PARRDR>REMARKS  the csd-derived protein parameters of Engh and Huber.  For use 
 PARRDR>REMARKS  with PARAMCSDX_MOD.PRO.  New atom type CC6 for exocyclic 6 carbon 
 PARRDR>REMARKS  Bill Weis 5/11/92 
 PARRDR> 
 PARRDR>set echo=false end 
 PARRDR> 
 PARRDR>  end 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
 CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN> 
 CHAIN>   coordinates @1.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 1.pdb opened.
 COOR>ATOM      1  N   ILE     8      49.186  33.900  14.272  1.00 15.00 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:    32 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=        270(MAXA=       36000)  NBOND=        277(MAXB=       36000)
 NTHETA=       404(MAXT=       50000)  NGRP=          34(MAXGRP=     36000)
 NPHI=         159(MAXP=       60000)  NIMPHI=       135(MAXIMP=     24000)  
 NDON=          44(MAXPAD=     10000)  NACC=          41(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      1 atoms have been selected out of    270
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of    270
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      1 atoms have been selected out of    270
 X-PLOR> 
 X-PLOR>   coordinates @1.pdb     {*Here we actually read the*} 
 ASSFIL: file 1.pdb opened.
 COOR>ATOM      1  N   ILE     8      49.186  33.900  14.272  1.00 15.00 
 COOR>ATOM      2  CD1 ILE     8      50.755  35.272  17.630  1.00 15.00 
 %READC-ERR: still     43 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
 CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN> 
 CHAIN>   coordinates @2.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 2.pdb opened.
 COOR>ATOM    228  N   ILE    41      43.788  31.593  22.173  1.00 15.00 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:    32 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=        549(MAXA=       36000)  NBOND=        560(MAXB=       36000)
 NTHETA=       814(MAXT=       50000)  NGRP=          68(MAXGRP=     36000)
 NPHI=         312(MAXP=       60000)  NIMPHI=       273(MAXIMP=     24000)  
 NDON=          93(MAXPAD=     10000)  NACC=          86(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      1 atoms have been selected out of    549
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of    549
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      1 atoms have been selected out of    549
 X-PLOR> 
 X-PLOR>   coordinates @2.pdb     {*Here we actually read the*} 
 ASSFIL: file 2.pdb opened.
 COOR>ATOM    228  N   ILE    41      43.788  31.593  22.173  1.00 15.00 
 COOR>ATOM    229  CD1 ILE    41      39.529  31.928  24.351  1.00 15.00 
 %READC-ERR: still     92 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
 CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN> 
 CHAIN>   coordinates @3.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 3.pdb opened.
 COOR>ATOM    457  CB  ALA    74      43.158  16.211  37.281  1.00 15.00 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:    24 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=        736(MAXA=       36000)  NBOND=        751(MAXB=       36000)
 NTHETA=      1091(MAXT=       50000)  NGRP=          94(MAXGRP=     36000)
 NPHI=         414(MAXP=       60000)  NIMPHI=       370(MAXIMP=     24000)  
 NDON=         122(MAXPAD=     10000)  NACC=         119(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      1 atoms have been selected out of    736
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of    736
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      0 atoms have been selected out of    736
 X-PLOR> 
 X-PLOR>   coordinates @3.pdb     {*Here we actually read the*} 
 ASSFIL: file 3.pdb opened.
 COOR>ATOM    457  CB  ALA    74      43.158  16.211  37.281  1.00 15.00 
 COOR>ATOM    458  C   ALA    74      43.390  18.122  38.901  1.00 15.00 
 %READC-ERR: still    121 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
 CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN> 
 CHAIN>   coordinates @4.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 4.pdb opened.
 COOR>ATOM    615  CB  ALA   100      58.051  37.875  28.748  1.00 15.00 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:     7 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=        781(MAXA=       36000)  NBOND=        795(MAXB=       36000)
 NTHETA=      1157(MAXT=       50000)  NGRP=         103(MAXGRP=     36000)
 NPHI=         436(MAXP=       60000)  NIMPHI=       390(MAXIMP=     24000)  
 NDON=         131(MAXPAD=     10000)  NACC=         127(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      1 atoms have been selected out of    781
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of    781
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      0 atoms have been selected out of    781
 X-PLOR> 
 X-PLOR>   coordinates @4.pdb     {*Here we actually read the*} 
 ASSFIL: file 4.pdb opened.
 COOR>ATOM    615  CB  ALA   100      58.051  37.875  28.748  1.00 15.00 
 COOR>ATOM    616  C   ALA   100      59.426  39.396  27.289  1.00 15.00 
 %READC-ERR: still    130 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain @/sgi/local/xtal/xplor3.8/toppar/toph19.pep 
 ASSFIL: file /sgi/local/xtal/xplor3.8/toppar/toph19.pep opened.
 CHAIN>REMARKS  TOPH19.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN>          
 CHAIN>   coordinates @5.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 5.pdb opened.
 COOR>ATOM    651  CB  ALA   111      37.082  48.685  28.204  1.00 15.00 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:    67 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1371(MAXA=       36000)  NBOND=       1398(MAXB=       36000)
 NTHETA=      2030(MAXT=       50000)  NGRP=         172(MAXGRP=     36000)
 NPHI=         766(MAXP=       60000)  NIMPHI=       689(MAXIMP=     24000)  
 NDON=         240(MAXPAD=     10000)  NACC=         206(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      1 atoms have been selected out of   1371
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of   1371
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      4 atoms have been selected out of   1371
 X-PLOR> 
 X-PLOR>   coordinates @5.pdb     {*Here we actually read the*} 
 ASSFIL: file 5.pdb opened.
 COOR>ATOM    651  CB  ALA   111      37.082  48.685  28.204  1.00 15.00 
 COOR>ATOM    652  C   ALA   111      37.246  47.359  30.216  1.00 15.00 
 %READC-ERR: still    239 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain 
 CHAIN>          
 CHAIN>   coordinates @6.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 6.pdb opened.
 COOR>ATOM   1132  C1  NAG   301      51.140  33.159  50.368  1.00 15.00 
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:     1 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1401(MAXA=       36000)  NBOND=       1428(MAXB=       36000)
 NTHETA=      2083(MAXT=       50000)  NGRP=         173(MAXGRP=     36000)
 NPHI=         780(MAXP=       60000)  NIMPHI=       696(MAXIMP=     24000)  
 NDON=         245(MAXPAD=     10000)  NACC=         212(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      0 atoms have been selected out of   1401
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      0 atoms have been selected out of   1401
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      0 atoms have been selected out of   1401
 X-PLOR> 
 X-PLOR>   coordinates @6.pdb     {*Here we actually read the*} 
 ASSFIL: file 6.pdb opened.
 COOR>ATOM   1132  C1  NAG   301      51.140  33.159  50.368  1.00 15.00 
 COOR>ATOM   1133  C2  NAG   301      50.914  31.796  49.679  1.00 15.00 
 %READC-ERR: still    254 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> segment                                              {*Generate first bit.*} 
 SEGMENT> 
 SEGMENT>   name="    "                              {*This name has to match the   *} 
 SEGMENT>                                            {*four characters in columns 73*} 
 SEGMENT>                                            {*through 76 in the coordinate *} 
 SEGMENT>                                            {*file; in XPLOR this name is  *} 
 SEGMENT>                                            {*referred to as SEGId.        *} 
 SEGMENT> 
 SEGMENT>   chain 
 CHAIN>          
 CHAIN>   coordinates @7.pdb           {*interpret coordinate file to*} 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file 7.pdb opened.
 COOR>ATOM   1146  C1  NAG   302      50.629  38.155  47.096  1.00 15.00 
 CHAIN>           {*interpret coordinate file to*} 
 CHAIN>   end                             {*obtain the sequence.        *} 
 SEGMENT> end 
 SEGMNT:     1 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1431(MAXA=       36000)  NBOND=       1458(MAXB=       36000)
 NTHETA=      2136(MAXT=       50000)  NGRP=         174(MAXGRP=     36000)
 NPHI=         794(MAXP=       60000)  NIMPHI=       703(MAXIMP=     24000)  
 NDON=         250(MAXPAD=     10000)  NACC=         218(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>                                                 {*Sometimes different atom*} 
 X-PLOR> vector do (name="O") ( name OT1 )               {*names are used.         *} 
 SELRPN:      0 atoms have been selected out of   1431
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      0 atoms have been selected out of   1431
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:      0 atoms have been selected out of   1431
 X-PLOR> 
 X-PLOR>   coordinates @7.pdb     {*Here we actually read the*} 
 ASSFIL: file 7.pdb opened.
 COOR>ATOM   1146  C1  NAG   302      50.629  38.155  47.096  1.00 15.00 
 COOR>ATOM   1147  C2  NAG   302      50.947  38.411  48.585  1.00 15.00 
 %READC-ERR: still    269 missing coordinates (in selected subset)
 X-PLOR>     {*Here we actually read the*} 
 X-PLOR>                                            {*coordinates.             *} 
 X-PLOR> 
 X-PLOR>{*-------------------------------------------------------------------------*} 
 X-PLOR> 
 X-PLOR>{===>}                                               {*Create S-S bridges.*} 
 X-PLOR> patch disu 
 PATCH>   reference=1=( resid 76 ) 
 SELRPN:      7 atoms have been selected out of   1431
 PATCH>   reference=2=( resid 175 ) 
 SELRPN:      7 atoms have been selected out of   1431
 PATCH> end 
 MAPIC: Atom numbers being modified
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1431(MAXA=       36000)  NBOND=       1459(MAXB=       36000)
 NTHETA=      2138(MAXT=       50000)  NGRP=         176(MAXGRP=     36000)
 NPHI=         797(MAXP=       60000)  NIMPHI=       703(MAXIMP=     24000)  
 NDON=         250(MAXPAD=     10000)  NACC=         218(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>{===>}                                               {*Create NAG ASN link.*} 
 X-PLOR> patch B1N 
 PATCH>   reference=1=( resid 65 ) 
 SELRPN:     11 atoms have been selected out of   1431
 PATCH>   reference=2=(resid 301 ) 
 SELRPN:     30 atoms have been selected out of   1431
 PATCH> end 
 %PATCH-ERR: atom +ND2  not found
 %PATCH-ERR: atom +HD22 not found
 %PATCH-ERR: atom +HD21 not found
 %PATCH-ERR: atom -C1   not found
 %PATCH-ERR: atom -O1   not found
 %PATCH-ERR: atom -HO1  not found
 %PATCH-ERR: bond -C1   +ND2  not found 
 %PATCH-ERR: angle +CG   +ND2  -C1   not found 
 %PATCH-ERR: angle +HD22 +ND2  -C1   not found 
 %PATCH-ERR: angle +ND2  -C1   -C2   not found 
 %PATCH-ERR: angle +ND2  -C1   -O5   not found 
 %PATCH-ERR: angle +ND2  -C1   -H1   not found 
 %PATCH-ERR: dihedral +CG   +ND2  -C1   -H1   not found
 %PATCH-ERR: improper +ND2  -C1   +HD22 +CG   not found
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1431(MAXA=       36000)  NBOND=       1459(MAXB=       36000)
 NTHETA=      2138(MAXT=       50000)  NGRP=         176(MAXGRP=     36000)
 NPHI=         797(MAXP=       60000)  NIMPHI=       703(MAXIMP=     24000)  
 NDON=         250(MAXPAD=     10000)  NACC=         218(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR> patch B14                                           {*Create NAG NAG bond.*} 
 PATCH>   reference=1=( resid 301 ) 
 SELRPN:     30 atoms have been selected out of   1431
 PATCH>   reference=2=( resid 302 ) 
 SELRPN:     30 atoms have been selected out of   1431
 PATCH> end 
 %PATCH-ERR: atom +O4   not found
 %PATCH-ERR: atom +C4   not found
 %PATCH-ERR: atom +HO4  not found
 %PATCH-ERR: atom -C1   not found
 %PATCH-ERR: atom -O1   not found
 %PATCH-ERR: atom -HO1  not found
 %PATCH-ERR: bond -C1   +O4   not found 
 %PATCH-ERR: angle +C4   +O4   -C1   not found 
 %PATCH-ERR: angle +O4   -C1   -H1   not found 
 %PATCH-ERR: angle +O4   -C1   -O5   not found 
 %PATCH-ERR: angle +O4   -C1   -C2   not found 
 %PATCH-ERR: dihedral +C4   +O4   -C1   -H1   not found
 %PATCH-ERR: dihedral +C4   +O4   -C1   -O5   not found
 %PATCH-ERR: dihedral +C4   +O4   -C1   -C2   not found
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1431(MAXA=       36000)  NBOND=       1459(MAXB=       36000)
 NTHETA=      2138(MAXT=       50000)  NGRP=         176(MAXGRP=     36000)
 NPHI=         797(MAXP=       60000)  NIMPHI=       703(MAXIMP=     24000)  
 NDON=         250(MAXPAD=     10000)  NACC=         218(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR>{===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray } 
 X-PLOR>        { crystallography or modelling.  Set the FALSE for most X-ray     } 
 X-PLOR>        { crystallographic applications at resolution > 1. A              } 
 X-PLOR> evaluate ($hydrogen_flag=FALSE) 
 EVALUATE: symbol $HYDROGEN_FLAG set to FALSE (logical)
 X-PLOR> 
 X-PLOR> if ($hydrogen_flag=TRUE) then 
 NEXTCD: condition evaluated as false
 X-PLOR>    flags exclude vdw elec end                {*Do QUICK hydrogen building w/o*} 
 X-PLOR>                                              {*vdw and elec terms.           *} 
 X-PLOR>    hbuild                                      {*This statement builds       *} 
 X-PLOR>       selection=( hydrogen )                   {*missing hydrogens, which are*} 
 X-PLOR>       phistep=45                               {*needed for the force field. *} 
 X-PLOR>    end 
 X-PLOR> 
 X-PLOR>    constraints fix=( not hydrogen ) end      {* Minimize hydrogen positions. *} 
 X-PLOR>    flags include vdw end 
 X-PLOR>    minimize powell 
 X-PLOR>       nstep=40 
 X-PLOR>    end 
 X-PLOR>    constraints fix=( not all ) end 
 X-PLOR> else 
 X-PLOR>    delete selection=( hydrogen ) end 
 SELRPN:    270 atoms have been selected out of   1431
 MAPIC: Atom numbers being modified
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       1161(MAXA=       36000)  NBOND=       1189(MAXB=       36000)
 NTHETA=      1627(MAXT=       50000)  NGRP=         176(MAXGRP=     36000)
 NPHI=         707(MAXP=       60000)  NIMPHI=       535(MAXIMP=     24000)  
 NDON=           0(MAXPAD=     10000)  NACC=         218(MAXPAD=     10000)
 NNB=            0(MAXNB=       4000) 
 X-PLOR> end if 
 X-PLOR> 
 X-PLOR> {* Set occupancies and b-factors if necessary *} 
 X-PLOR> vector do (q=1.0 ) ( all ) 
 SELRPN:   1161 atoms have been selected out of   1161
 X-PLOR> vector do (b=15.)  ( all ) 
 SELRPN:   1161 atoms have been selected out of   1161
 X-PLOR> 
 X-PLOR> write coordinates output=model12_gen.pdb end         {*Write out coordinates.*} 
 ASSFIL: file model12_gen.pdb opened.
 X-PLOR> write structure output=model12.psf end           {*Write out structure file.*} 
 ASSFIL: file model12.psf opened.
 X-PLOR> stop 
 CSTACK: size=    40000 used=     2912 current=        0
 HEAP:   maximum use=    71493 current use=        0
 X-PLOR: total CPU time=      2.5009 s
 X-PLOR: entry time at 19:50:06 30-Apr-98
 X-PLOR: exit time at 19:50:14 30-Apr-98


{*-----------------------------------------------------------------------------------*}
	input pdb files
{*-----------------------------------------------------------------------------------*}

	{*---------------------------------------------*}
		Excerpt from 2.pdb
	{*---------------------------------------------*}

ATOM    403  N   ASN    65      48.464  42.545  42.942  1.00 15.00
              
ATOM    404  ND2 ASN    65      50.062  38.786  45.595  1.00 15.00
              
ATOM    405  OD1 ASN    65      50.951  39.678  43.765  1.00 15.00
              
ATOM    406  CG  ASN    65      50.133  39.733  44.687  1.00 15.00
              
ATOM    407  CB  ASN    65      49.155  40.925  44.729  1.00 15.00
              
ATOM    408  CA  ASN    65      48.520  41.195  43.410  1.00 15.00
              
ATOM    409  C   ASN    65      47.505  40.223  42.913  1.00 15.00
              
ATOM    410  O   ASN    65      46.788  39.591  43.733  1.00 15.00
              

	{*---------------------------------------------*}
		sugar input files 6 and 7.pdb
	{*---------------------------------------------*}
ATOM   1132  C1  NAG   301      51.140  33.159  50.368  1.00 15.00
              
ATOM   1133  C2  NAG   301      50.914  31.796  49.679  1.00 15.00
              
ATOM   1134  C3  NAG   301      50.457  30.700  50.646  1.00 15.00
              
ATOM   1135  C4  NAG   301      51.377  30.689  51.857  1.00 15.00
              
ATOM   1136  C5  NAG   301      51.365  32.058  52.555  1.00 15.00
              
ATOM   1137  C6  NAG   301      52.218  32.182  53.834  1.00 15.00
              
ATOM   1138  C7  NAG   301      50.067  31.460  47.387  1.00 15.00
              
ATOM   1139  C8  NAG   301      48.981  31.633  46.334  1.00 15.00
              
ATOM   1140  N2  NAG   301      49.894  31.935  48.632  1.00 15.00
              

ATOM   1141  O3  NAG   301      50.594  29.477  49.901  1.00 15.00              

ATOM   1142  O4  NAG   301      50.918  29.699  52.763  1.00 15.00              

ATOM   1143  O5  NAG   301      51.846  33.024  51.609  1.00 15.00              

ATOM   1144  O6  NAG   301      53.586  32.061  53.490  1.00 15.00              

ATOM   1145  O7  NAG   301      51.106  30.858  47.092  1.00 15.00              

ATOM   1146  O1  NAG   301      50.062  38.786  45.595  1.00 15.00

END


ATOM   1146  C1  NAG   302      50.629  38.155  47.096  1.00 15.00              

ATOM   1147  C2  NAG   302      50.947  38.411  48.585  1.00 15.00              

ATOM   1148  C3  NAG   302      51.507  37.179  49.303  1.00 15.00              

ATOM   1149  C4  NAG   302      50.613  35.983  49.009  1.00 15.00              

ATOM   1150  C5  NAG   302      50.532  35.731  47.495  1.00 15.00              

ATOM   1151  C6  NAG   302      49.697  34.513  47.049  1.00 15.00              

ATOM   1152  C7  NAG   302      51.581  40.787  48.776  1.00 15.00              

ATOM   1153  C8  NAG   302      52.642  41.873  48.889  1.00 15.00              

ATOM   1154  N2  NAG   302      51.934  39.493  48.701  1.00 15.00              

ATOM   1155  O3  NAG   302      51.451  37.515  50.700  1.00 15.00              

ATOM   1156  O4  NAG   302      51.166  34.841  49.644  1.00 15.00              

ATOM   1157  O5  NAG   302      49.960  36.902  46.896  1.00 15.00              

ATOM   1158  O6  NAG   302      48.336  34.748  47.361  1.00 15.00              

ATOM   1159  O7  NAG   302      50.386  41.105  48.774  1.00 15.00              

ATOM   1160  O1  NAG   302      50.918  29.699  52.763  1.00 15.00

END







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