[gmx-users] protein with multiple chains

[David]

On Wed, 2004-10-20 at 17:45, Andre Farias de Moura wrote:
> On Wed, 20 Oct 2004, Jair wrote:
> 
> > Ok, I have tried this too, but make_ndx do not found the chains:
> > *****
> > Opening library file /chem/gromacs-3.2.1/share/top/aminoacids.dat
> > There are: 15955   OTHER residues
> > There are:  382  PROTEIN residues
> > There are:   0    DNA residues
> > Analysing Protein...
> > Analysing Other...
> >
> >  0 System       : 54004 atoms
> >  1 Protein       : 6155 atoms
> >  2 Protein-H      : 3094 atoms
> >  3 C-alpha       :  382 atoms
> >  4 Backbone      : 1146 atoms
> >  5 MainChain      : 1532 atoms
> >  6 MainChain+Cb    : 1892 atoms
> >  7 MainChain+H     : 1896 atoms
> >  8 SideChain      : 4259 atoms
> >  9 SideChain-H     : 1562 atoms
> > 10 Prot-Masses     : 6155 atoms
> > 11 Non-Protein     : 47849 atoms
> > 12 SOL         : 47841 atoms
> > 13 NA+         :   8 atoms
> > 14 Other        : 47849 atoms
> > *******
> > Shoud I edit some other file?
> 
> 
> use the option which selects atoms based on their
> numbers (check your pdb file to see the range for
> each chain).
Or use the output pdb file from pdb2gmx (pdb2gmx -q out.pdb) as  input
for make_ndx

> 
> best regards,
> 
> andre'
> 
> 
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> 
>     Dr. Andre' Farias de Moura
> 
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> 
>   Laboratorio de Quimica Teorica
> Universidade Federal de Sao Carlos
>      Sao Carlos - SP - Brasil
> 
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> 
>         Endereco Atual
> 
>     Grupo de Quimica Quantica
> Instituto de Quimica de Sao Carlos
>     Universidade de Sao Paulo
>     Sao Carlos - SP - Brasil
>     Telefone: 55-16-3373-8055
> 
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> 
> >
> > On Wednesday 20 October 2004 14:50, jjvcirino at ig.com.br wrote:
> > > A have a question about how to simulate a protein with multiple chains.
> > > In the original pdb file the chains are identified with the letters W, V,
> > > X, and Y.
> > > When I processed this file with pdb2gmx:
> > >
> > >  pdb2gmx -ss -f prot.pdb -o prot.gro -p prot.top
> > >
> > > the resulting .gro file did not contain any explicit (to me) information
> > > about
> > > each chain. All residues are written
> > > sequentially. But four itp files are generated.
> > > When I tried to run grommp:
> > >
> > >  grompp -f md.mdp -c prot_md.gro -p prot.top -o prot_md.tpr -np 4
> > >
> > > with the following options in the .mdp file:
> > >
> > >  energygrps       = Protein_W  Protein_V  Protein_X  Protein_Y
> > > SOL  NA+
> > >  tc-grps           = Protein_W  Protein_V  Protein_X
> > > Protein_Y  SOL  NA+
> > >  tau_t            = 0.1  0.1  0.1  0.1  0.1  0.1
> > >  ref_t            = 300  300  300  300  300  300
> > >
> > > I got an error:
> > >
> > >  processing topology...
> > >  Generated 243951 of the 243951 non-bonded parameter combinations
> > >  Generating 1-4 interactions: fudge = 0.5
> > >  Generated 243951 of the 243951 1-4 parameter combinations
> > >  Cleaning up temporary file gromppYGHL8M
> > >  Fatal error: No such moleculetype Protein_V
> > >
> > > What can I do to calculate the interaction energies between each chain?
> > > I watched the mailing lists but I did not find the solution.
> > > Thanks for the help.
> > >
> > > JJVC
> > > e-mail: jair at iq.ufrj.br
> > > Depto. Qumica Orgnica
> > > IQ-UFRJ
> > > Rio de Janeiro - Brazil
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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