VMD-L Mailing List

From: MW Van der Kamp, School of Chemistry (Marc.VanderKamp_at_bristol.ac.uk)
Date: Fri May 05 2006 - 09:50:23 CDT

Hi John,

I'm running version 1.8.3 on the moment.
But I gather from your reaction that CHARMM psf files can't be written yet.
I got my hopes up after finding the following post in the VMD-l archive:

***************
On Dec 3, 2003, at 10:05 PM, Mike McCallum wrote:

>
> I seem to remember asking this question before, but I can't seem to
> find any answer, so here goes:
>
> Using psfgen through vmd and tkcon is really a great thing, but what
> if you want to use the psf file in charmm? Charmm will *write* XPLOR
> format psf, but not read. Will psfgen generate charmm-type psf files?
> I'm almost sure that it can, but I can't find it in the docum

Yes:

writepsf charmm foo.psf

will write in charmm format. "writepsf x-plor foo.psf" will write in
x-plor format, as will "writepsf foo.psf".

Cheers,
Justin
******************

Thanks for your reaction, and I hope writing charmm psf-files will be added
as a feature in a next version of VMD.. ;)

Marc

--On 05 May 2006 09:42 -0500 John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Marc,
> Which version of VMD are you running? ('vmdinfo version' will tell you
> if it's not clear)
> The PSF files written by VMD atom selections (in the current version)
> will lack angles, dihedrals, impropers, and cross-terms. Also, there's
> no "charmm" keyword currently. The right syntax is:
> set sel [atomselect top all]
> $sel writepsf test.psf
>
> Thanks,
> John stone
> vmd_at_ks.uiuc.edu
>
> On Fri, May 05, 2006 at 03:02:37PM +0100, MW Van der Kamp, School of
> Chemistry wrote:
>> Hi,
>>
>> > From what I thought and previous posts, one should be able to write a
>> psf-file in CHARMM format by making a selection of all atoms ('set all
>> [atomselect top all]') and then use the following:
>>
>> $all writepsf charmm test.psf
>>
>> When I try this however, I get 'atomselection: improper method:
>> writepsf'... What am I doing wrong?
>>
>> Thanks in advance for any help,
>> Marc
>>
>> ---------------------------------------------------
>> Marc van der Kamp, PhD-student
>> School of Chemistry, Research group of Dr. Adrian Mulholland
>> University of Bristol
>> E-mail: Marc.vanderKamp_at_bristol.ac.uk
>>
>
> --
> 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

---------------------------------------------------
Marc van der Kamp, PhD-student
School of Chemistry, Research group of Dr. Adrian Mulholland
University of Bristol
E-mail: Marc.vanderKamp_at_bristol.ac.uk