[gmx-users] Potein-protein complex simulations

Lucio Ricardo Montero Valenzuela lucioric at ibt.unam.mx
Thu Apr 8 18:11:15 CEST 2010

If you are working with a two-protein complex, you don't need PRODRG.
You can create the complex topology in pdb2gmx using as input a PDB file
with two chains, each chain for a protein. Then pdb2gmx does the job of
creating an itp file for each protein, and a top file for the complex,
which has #include statements for the itp files.
Best regards.
Lucio Montero
Dr. Federico Sánchez Lab
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210

El jue, 08-04-2010 a las 00:01 -0700, pawan raghav escribió:
> Dear users,
>                   I am using gromacs to understand the protein-protein
> complex interaction stability prediction. for this I have used
> protein-protein docked complex as initial .pdb file to simulate.
> According to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file
> needed as input for drug molecule as seperate from protein file. So
> please tell me is this compulsory to use small molecule as seperate,
> or can I perform MD simulation by taking complex structure as
> directly. I am little confuse about to do this because if I choose
> this then problem will occurs with calculating the g_hbond. the
> g_hbond analyze the H-bonds between the complex and with complex only.
> But I am intrested to calculate the H-bonds between the protein
> (receptor) and and protein (ligand). Please notify me how can I make
> this possible if no then tell me how to make .itp file of protein
> (ligand) without using PRODRUG2 SERVER. Because prodrug server
> produced the .itp file other than default amino acids example DRG.
> -- 
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