Reordering of atoms in Generate..

Mark Roe roe at biochemistry.ucl.ac.uk
Fri Apr 3 04:30:24 EST 1998


Hi All,

I am trying to run NCS restraints in X-PLOR 3.851. However when I generate
my DNA strands, the first always has some atoms reordered in every base in
the strand in the output pdb file. Thus the NCS fails because the atoms
are not serially identical. I have never seen this problem with protein
files, so I presume my DNA setup is not correct?

Does anyone know why generate does this and how to avoid it?
(generate.inp file is at the bottom of this message.)

Cheers,
Mark Roe.

Dr. S. M. Roe,
LICR/UCL X-ray Crystallography Laboratory,
Department of Biochemistry,
University College London,
Gower Street,
London.
WC1E 6BT.

Tel. (44) 171 504 2303
Fax. (44) 171 380 7193

E-mail roe at biochem.ucl.ac.uk

____________________________________________________________________________
____________________________________________________________________________


 remarks  file  generate/generate.inp
 remarks  Generate structure file and hydrogens for a protein

 topology  @TOPPAR:tophcsdx.pro
           @TOPPAR:dna-rna.top
           end                                        {*Read topology file.*}                     
 parameter 

@TOPPAR:protein_rep.param                        {*Read empirical potential*}
@TOPPAR:dna-rna_rep.param                        {*parameter file CHARMM19 *}
                                                 {*with modifications.     *}
 end

 segment                                                {*Generate protein.*}

   name="AAAA"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaaa.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaaa.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAB"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaab.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaab.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAC"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaac.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaac.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAD"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaad.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaad.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}
						
 segment                                                {*Generate protein.*}

   name="AAAE"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaae.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaae.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAF"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaaf.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaaf.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAG"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaag.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaag.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

 segment                                                {*Generate protein.*}

   name="AAAH"                              
   chain
     LINK NUC HEAD - * TAIL + * END
     FIRST 5TER TAIL + * END                   {* phosphorylated 5' end *}
     LAST 3TER   HEAD - * END
     coordinates @test_aaah.pdb              {*interpret coordinate file to*}
   end                                       {*obtain the sequence.        *}
 end

 for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
    patch deox reference=nil=( resid $1 ) end
 end loop main
                                            
 coordinates @test_aaah.pdb                     {*Here we actually read the*}
                                                {*coordinates.             *}

                                             
 {===>} {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=TRUE)
 
        
 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 and not known)      {*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 ) ( attribute q # 1.0 ) }
 vector do (b=80.)  ( attribute b > 80. )
 vector do (b=10.)  ( attribute b < 10. )


{===>}
 write coordinates output=junk.pdb end        {*Write out coordinates.*} 

{===>}
 write structure output=junk.psf end       {*Write out structure file.*}
 stop





More information about the X-plor mailing list