[gmx-users] Generating topology

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 22 06:15:37 CET 2012

On 22/03/2012 2:54 PM, Spring buds wrote:
> Hi
> A protein sits on the top of another protein (not docking). I then 
> used pdb2gmx command to generate the topology. Surprisingly, i got 
>  five files, as given below: I think the two proteins are not 
> connected each other. is it possible to make it one posre and topol file.

Yes, see discussion in pdb2gmx -h. (Checking -h should always been a 
first place to look for information)


> Many thanks in advance
> posre_Protein_chain_A.itp
> posre_Protein_chain_A2.itp
> topol.top
> topol_Protein_chain_A.itp
> topol_Protein_chain_A2.itp

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