Re: [AMBER] production error.

From: David Case <>
Date: Tue, 14 Feb 2017 12:15:36 -0500

On Tue, Feb 14, 2017, Saman Yousuf ali wrote:

> I have also visualized
> trajectories before and after re-imaging using vmd. In both cases, after
> few frames one monomer move away from another. Both chains are not
> bonded with each other but are very close. I am unable to understand
> this issue. You told me that I should specify anchor molecule for
> re-imaging. My target system consists of chain A 1-267 residues, chain B
> 268-354 residues, co-factor and ligand of chain A 355-356, and co-factor
> and ligand of chain B 357-358 molecules. Can you please suggest me
> anchor molecule for my case. 

Sounds like you should image only the solvent, keeping both chains and both
ligands fixed. Others on the list are probably more experienced in this and
may have better suggestions.

If things don't work, be sure to post the exact commands you gave to cpptraj:
there is often an important distinction between what you intended to do, and
what you actually did.


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Received on Tue Feb 14 2017 - 09:30:02 PST
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