VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Sep 30 2016 - 11:39:04 CDT

You can always save the structure at any time from the "File" menu by using
"Save Coordinates..." or by making an atom selection and using the writepdb
command. Also, if you are using the chirality plugin and running namd after
each correction, you should already have the new pdb in whatever directory
namd is being run.

On Fri, Sep 30, 2016 at 2:36 AM jrhau lung <jrhaulung_at_gmail.com> wrote:

> Dear VMD-I friends:
> Probably due to the homology based structure modeling, the outcome
> protein structure contains many amino acids do not pass the VMD chirality
> checkup and need to be manually correct them one by one. Is there a way to
> update the psf and pdb file after several correction steps? Since a crash
> in the MD structure optimization after chirality correction will make the
> structure repairment work to be started all over again. Thanks!
>
> sincerly,
>
> Jrhau
>