problem using @TOPPAR:charmm22/toph22.pep

Dr.Z.P. Han z.p.han at uea.ac.uk
Thu Jun 26 12:30:53 EST 1997


Dear X-Plorers,

X-Plor complained that
 %PATCH-ERR: dihedral -CB   -CA   -C    -OT2  not found
 %PATCH-ERR: dihedral -CB   -CA   -C    -OT1  not found
 %PATCH-ERR: dihedral -HA   -CA   -C    -OT2  not found
 %PATCH-ERR: dihedral -HA   -CA   -C    -OT1  not found
when generating hydrogens for a protein segment with GLY C-terminal. 
Could any one help on this or explain causes?  Part of generate.inp used
as follows (command:  xplor < generate.inp).
--------------------------------------------------------------------------------------

 X-PLOR> {* segment 1b *}						 
 X-PLOR> segment                                               
{*Generate protein.*} 
 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>   chain 
 CHAIN>     @TOPPAR:charmm22/toph22.pep            {*Read peptide bond
file;     *} 
 ASSFIL: file /inet/chesg8-sw1/nmr/xplor3.843/toppar/charmm22/toph22.pep
opened.
 CHAIN>REMARKS  TOPH22.pep -MACRO for protein sequence 
 CHAIN>SET ECHO=FALSE END 
 CHAIN> 
 CHAIN>            {*Read peptide bond file;     *} 
 CHAIN>     coordinates @/home/che/zph/XPLOR/unit1b.pdb 
 SEGMNT: sequence read from coordinate file
 ASSFIL: file /home/che/zph/XPLOR/unit1b.pdb opened.
 COOR>ATOM   1301  N   MET B  1B      73.718 100.072  20.503  1.00  6.07 
 MAPIC: Atom numbers being modified
 MAPIC: Atom numbers being modified
 %PATCH-ERR: dihedral -CB   -CA   -C    -OT2  not found
 %PATCH-ERR: dihedral -CB   -CA   -C    -OT1  not found
 %PATCH-ERR: dihedral -HA   -CA   -C    -OT2  not found
 %PATCH-ERR: dihedral -HA   -CA   -C    -OT1  not found
 CHAIN>                                             {*interpret
coordinate file to*} 
 CHAIN>   end                                       {*obtain the
sequence.        *} 
 SEGMENT> end 
 SEGMNT:   158 residues were inserted into segment "    "
 XPLOR: current counts (number in parenthesis is maximum)
 NATOM=       5161(MAXA=       36000)  NBOND=       5199(MAXB=      
36000)
 NTHETA=      9400(MAXT=       50000)  NGRP=        1536(MAXGRP=    
36000)
 NPHI=       14063(MAXP=       60000)  NIMPHI=       878(MAXIMP=    
24000)  
 NDON=         575(MAXPAD=     10000)  NACC=         503(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   5161
 X-PLOR> vector do (name="OT") ( name OT2 ) 
 SELRPN:      1 atoms have been selected out of   5161
 X-PLOR> vector do (name="CD1") ( name CD and resname ile ) 
 SELRPN:     12 atoms have been selected out of   5161
 X-PLOR> 
 X-PLOR> coordinates @/home/che/zph/XPLOR/unit1b.pdb 
 ASSFIL: file /home/che/zph/XPLOR/unit1b.pdb opened.
 COOR>ATOM   1301  N   MET B  1B      73.718 100.072  20.503  1.00  6.07 
 COOR>ATOM   1302  CA  MET B  1B      72.976 101.319  20.817  1.00  6.77 
 %READC-ERR: still   2567 missing coordinates (in selected subset)
 X-PLOR>                                                {*Here we
actually read the*} 
 X-PLOR>                                               
{*coordinates.             *} 
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