Re: [AMBER] production error.

From: Saman Yousuf ali <>
Date: Tue, 14 Feb 2017 17:42:42 +0000 (UTC)

Dear David,I have used following command for re-imaging trajectories;parm complex.prmtoptrajin md_simulation1.mdcrd.gztrajin ...trajin ....trajin ....trajin ....trajin .....trajin .......trajin md_simulation50.mdcrd.gz
strip :NA+,WAT outprefix nowatertrajout reimaged-complex.mdcrd
In original script I have pasted trajin from md_simulation1.mdcrd.gz and so on but here I used dots just to shrink my script. Please help me to resolve this issue.
Thanks Best Regards, Saman Yousuf Ali

    On Tuesday, February 14, 2017 9:15 AM, David Case <> wrote:

 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 - 10:00:02 PST
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