VMD-L Mailing List
From: jrhau lung (jrhaulung_at_gmail.com)
Date: Mon Oct 03 2016 - 09:33:48 CDT
A erratum to previous message. Sorry for the mess.
A further question. When press Minimize/ equillbrate selected chiral
centers button, the console shows that a specific residue does not exist
and "skipping patch CTER". And then the console was crashed. I am pretty
sure that the residue does exist in both pdb and psf files. What would be
the potential cause for this. Thanks!
2016-10-03 22:17 GMT+08:00 jrhau lung <jrhaulung_at_gmail.com>:
> 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 <ryanmcgreevy_at_ks.uiuc.edu>:
>> 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!