VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Aug 31 2006 - 19:17:14 CDT

I got confused because of the writepsf command in psfgen package bearing
the same name. Now I can see the difference between both.
Thanks for your help
Cesar

John Stone escribió:
> This is correct..
> The 'writing' feature of the psf plugin was implemented to help users
> of SITUS who use PSF files for flexible fitting runs, where the PSF file
> is (ab)used for purposes it wasn't really intended to serve. I have begun
> extending the plugin interface in VMD to read and store the other data
> one finds in a PSF file, but it's hard to say if I'll ever go so far as
> to store everything that a PSF contains, or at least to store it in such
> a way that you'd be able to do what you're attempting to do. If enough people
> want to be able to do that, I'll consider it, but psfgen is surely the
> better long-term way of doing these sorts of transformations on PSF files.
> Perhaps we need to write a wrapper script for psfgen that does
> the operation that you're attempting with an interface as simple
> as what one can do with atom selections.
>
> John
>
> On Thu, Aug 31, 2006 at 06:51:43PM -0400, Axel Kohlmeyer wrote:
>
>> On 8/31/06, Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar> wrote:
>>
>>> Please help me because I am surely doing something wrong. I am using VMD
>>> 1.8.4 under Linux.
>>> I load a both psf and pdb files from the shell for a protein in a water
>>> box.
>>>
>>> $ vmd protein.psf protein.pdb
>>>
>>> I want to remove all the water so now from the tk console I put
>>> set prot [atomselect top protein]
>>>
>>> $prot writepsf prot.psf
>>> $prot writepdb prot.pdb
>>>
>>> Now if I take a look the psf from the shell
>>> $ grep angles protein.psf
>>> 66246 !NTHETA: angles
>>> $ grep angles prot.psf
>>> 0 !NTHETA: angles
>>>
>>>
>>> So, the angles have magically disapeared. The same happens to the
>>> dihedrals and impropers.
>>> Is this a bug or are there some steps that I am missing?
>>>
>> cesar,
>>
>> this is a 'feature': the psf reader in VMD does not read
>> and store the information as it is irrelevant for visualization,
>> only the bond information is read.
>>
>> my guess is, that you might get some help from the
>> autopsf tool for what you want.
>>
>> cheers,
>> axel.
>>
>>
>>> Regards
>>> Cesar
>>>
>>>
>>>
>> --
>> =======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>>
>
>