[gmx-users] Potein-protein complex simulations

[Mark Abraham]

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 
topologies.

> 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.

Mark