VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 03 2016 - 15:46:18 CDT

Hi,
  It would probably be helpful if you could provide a copy of the structure
that produces the problem and the exact steps you took so that someone
can try to reproduce the same issue. Once reproduced it would be much
easier to suggest what has gone wrong and/or how to get around it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 03, 2016 at 10:33:48PM +0800, jrhau lung wrote:
> 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 <[1]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 <[2]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 <[3]jrhaulung_at_gmail.com>
> wrote:
>
> Dear VMD-I friends:
> A A 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 A 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
> A to be started all over again. Thanks!
> sincerly,
> Jrhau
>
> References
>
> Visible links
> 1. mailto:jrhaulung_at_gmail.com
> 2. mailto:ryanmcgreevy_at_ks.uiuc.edu
> 3. mailto:jrhaulung_at_gmail.com 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/