VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Wed Oct 05 2016 - 20:17:05 CDT

Fix all chirality errors using Autodock tool byremove hydrogen and then add
hydrogen....

2016-10-04 4:46 GMT+08:00 John Stone <johns_at_ks.uiuc.edu>:

> 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/
>