[gmx-users] Potein-protein complex simulations

pawan raghav pwnrghv at gmail.com
Thu Apr 8 09:01:32 CEST 2010

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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