[gmx-users] protein with multiple chains

[David]

On Wed, 2004-10-20 at 18:50, 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 

You have to define the groups in the index file using make_ndx

> 
> 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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-- 
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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