[gmx-users] Potein-protein complex simulations
Mark.Abraham at anu.edu.au
Thu Apr 8 09:13:20 CEST 2010
On 8/04/2010 5:01 PM, pawan raghav wrote:
> 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
You need a topology for the whole system. It may be convenient to
generate the different [ moleculetype ] sections in different files and
#include them, or not. What's best depends on your sources of molecule
> 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
No, such issues are unrelated. g_hbond doesn't care about molecules, it
just looks for atomic contacts that occur between the sets you specified
with the index groups.
> 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
Read g_hbond -h and think about constructing suitable index groups to
use for this.
> 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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