Re: [AMBER] Help with imagining curled protein

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 13 Jul 2021 13:06:10 -0400

Hi,

Try 'autoimage' and see if that works for you. You can use it as-is,
or try specifying different expressions for the anchor mask.

This will only affect calculations that don't automatically perform
distance imaging. The 'hbond' calculation has imaging off by default,
but it can be turned on. Most calculations will automatically image
distances anyway - check the description in the manual to be certain.

-Dan

On Tue, Jul 13, 2021 at 10:00 AM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Dear Amber Community,
>
> My fairly straight, filamentous protein curled during dynamics, and I’m struggling to find a way to image it back into the box, if possible. I want to post-process the energetics with an implicit solvent, but I’m concerned that the results will be meaningless unless I figure out how to image the protein correctly. Because it’s a homotrimeric complex, I’ve tried the below script for imaging in cpptraj
>
> parm xxx.parm7
> reference xxx.rst7
> trajin xxx.mdcrd
> trajout yyy.mdcrd
>
> center :1-282 mass origin #domain 1
> image origin center
> center :1-564 mass origin #domain 1-2
> image origin center
> center :1-846 mass origin #domain 1-3
> image origin center
>
> But I still get the below (figures attached from 2 different frames). What can/should I try? How much of this issue is a visualization problem and won’t affect a non-periodic (implicit solvent) calculation?
>
> Best regards,
> Matthew
>
>
>
>
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Received on Tue Jul 13 2021 - 10:30:02 PDT
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