[gmx-users] protein with multiple chains

[Andre Farias de Moura]

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).

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. Química Orgânica
> > IQ-UFRJ
> > Rio de Janeiro - Brazil
>
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