From: jrhau lung (
Date: Mon Oct 03 2016 - 09:17:18 CDT

A further question. When press Minimize/ equillbrate selected chirral
centers button, the clone show that A specific Residue does not exist and
skiping patch CTER.
I am pretty sure that resid does exist in both pbd and psf, field. What
would be the potential cause for this. Thanks!

2016-10-01 0:39 GMT+08:00 Ryan McGreevy <>:

> 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 <> 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