Re: [AMBER] production error.

From: Saman Yousuf ali <>
Date: Tue, 14 Feb 2017 15:50:26 +0000 (UTC)

Dear David,Thanks for your kind response. 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. 
Thanks  Best Regards, Saman Yousuf Ali


    On Tuesday, February 14, 2017 6:15 AM, David Case <> wrote:

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

> then I added iwrap=1 flag and rerun siumlation using 26 rst file. When
> job finished, I reimaged mdcrd files using autoimage keyword and plotted
> rmsd as well. Upon loading reimaged trajectories into VMD, I observed
> that both subunitsdisplaced from their starting positon. After 8ns rmsd
> of dimer complex jumps from 5 to 25 angstroms.

Autoimage can sometime fail to find the desired "anchor" to which imaging
should be done, although it is in fact pretty smart.  You may need to specify
the anchor molecules yourself, so that one monomer in the dimer doesn't get
imaged relative to the other.  See the image commands in manual. 

And, of course, visualize your trajectory to see exactly what is
happening--that often makes clear things that seem curious or confusing if
all you are looking at is an RMSD vs. time plot.


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Received on Tue Feb 14 2017 - 08:00:02 PST
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