[gmx-users] protein with multiple chains

[Jair]

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?

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