[gmx-users] Generating topology

lina lina.lastname at gmail.com
Thu Mar 22 06:13:04 CET 2012

On Thu, Mar 22, 2012 at 11:54 AM, Spring buds <winterhot82 at gmail.com> 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.

You have already have one posre and topol.top

more topol.top
check what's inside your topol.top. pay attention to "include"
> 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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