From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 20 2009 - 13:34:12 CDT

namita,

please keep in mind that tools like VMD or psfgen have absolutely no
real knowledge of chemistry. they just do what you tell them to do,
i.e. what you have in your input files. quite often the resulting simulation
will run without complaints, but this is due to the kind of model that
you use that will allow the most ridiculous compounds to work, if you
build your topology this way.

obviously a thiolate sidechain with a hydrogen on the sulfur doesn't
make any sense chemically, so you must have made a mistake when
editing the topology file. it is impossible to debug those remotely,
so, again, have a close look at the description of the topology file
format in the topology tutorial and cross-check your modifications,
e.g. by comparing to the original unmodified residue. my guess
would be that you forgot to remove the hydrogen from the internal
coordinate section, or changed it in the wrong section of the file.

cheers,
    axel.

On Sun, Sep 20, 2009 at 9:50 AM, NAMITA BHADRA <namitabhadra_at_gmail.com> wrote:
> Hi,
>
> Thanks for reply. I am going through the Topology file
> tutorial.
>
> But now I create my PSF file through Auto-psf plug-in and the charge on the
> sulpher atom has been modified to -1.00 and I have decided to use this PSF
> file at the time of MD run. But there is a doubt in my mind that the
> hydrogen on SG atom is still present in the modified PSF file.
>
> Now my question is that may I use this modified PSF file for MD run? Please
> help.
>
>
>
> Thanks.
>
>
>
> Namita.
>
>
>
> On Thu, Sep 10, 2009 at 9:34 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>> PSF building isn't really my area of expertise, but if you need to make a
>> non-standard residue, you'll probably find it helpful to read the basic
>> NAMD tutorial (which also covers the basic use of psfgen),
>> and the topology file tutorial:
>> http://www.ks.uiuc.edu/Training/Tutorials/
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Wed, Sep 09, 2009 at 09:31:53AM +0530, NAMITA BHADRA wrote:
>> > Hi All,
>> >
>> >
>> >
>> > I am new in VMD.I want to create a PSF file of my
>> > protein
>> > having one cysteine residue as thiolate anion (want to delete the
>> > gamma
>> > hydrogen on sulpher atom) and one histidine as HSP state (keeping
>> > others
>> > as HSD state). How can I do these? Is it possible through autopsf
>> > plug-in?
>> > Please help me.
>> >
>> >
>> >
>> > Thanks in advance.
>> >
>> >
>> >
>> > Namita.
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.