[gmx-users] protein with multiple chains

jjvcirino at ig.com.br jjvcirino at ig.com.br
Wed Oct 20 18:50:55 CEST 2004

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 
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. 

e-mail: jair at iq.ufrj.br 
Depto. Química Orgânica 
Rio de Janeiro - Brazil 

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