VMD-L Mailing List

From: jrhau lung (jrhaulung_at_gmail.com)
Date: Wed Oct 05 2016 - 08:09:47 CDT

Fix all chirality error by Autodock tool using remove hydrogen and then add
hydrogen....

2016-10-04 6:54 GMT+08:00 jrhau lung <jrhaulung_at_gmail.com>:

> The pdb and psf files are uploaded in attached file. The psf file was
> generated by automatic psf builder (including everything, highlight XP1 and
> XO1 to create chains and press I'm feeling lucky). After that, the
> chirality plugin was launched from VMD extension, The hydrogen of residue
> LYS 5 was selected and moved. The problem showed up after pressing the
> Minimize/ equillbrate selected chiral centers button (using setting
> showed up in AutoIMD control and press submit), the console showed that the
> Residue 343 does not exist, "skipping patch CTER" and crashed. Hope
> these descriptions are enough. Thanks!
>
> 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/
>>
>
>