[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.
Dr. Federico Sánchez Lab
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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