VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 17 2009 - 14:37:13 CDT

On Fri, 2009-07-17 at 14:53 -0400, avl211_at_lehigh.edu wrote:

adrienne,

> Hello,
> I wrote earlier about having an issue with psfgen and a residue that
> was not being recognized by PSFGEN. Axel I tried what you suggested of
> atomselect residue names that were not MOL and then creating a pdb
> file from that and then going on to make a psf file. In doing that
> procedure that created the residue name MOL X and that still cannot be

i don't quite get this. how can your .pdb file can have a residue
named MOL, if you don't select it. either your description is not
correct, or you made a typo when executing the text interface commands.

> recognized by PSFGEN. So as you mentioned before I think I have a
> non-standard residue and I was wondering if you had any advice as to
> what to do with a non-standard residue when using PSFGEN? Thank you.

perhaps, i should not have used a "shortcut language" and ask for
more details and assume less about what you know or don't.

here is the basic modus operandi of psfgen:
psfgen can only produce a psf file for residues it knows about.
it uses the CHARMM format topology and residue database files for it,
and uses the residue (and atom) names to identify which residue template
to pick and how to generate atom position from internal coordinates,
if they are not already given (e.g. crystal structure files usually
don't have hydrogens, so those need to be added).

your compound obviously has something in it that is not yet in
the residue data base. how to proceed from here on depends on what
you want to do _after_ you have the .psf file generated.
do you want to run an MD? if yes, do you already have parameters
for your non-standard residue? if not, how do you plan to get them?
do you need the .psf for analysis? if yes, do you need angles,
dihedrals and so on?
or do you want to do something else?

as you can see, the amount of help somebody can give you, depends
a lot on the amount and detail of information you can provide about
what you want to do and how you intend to do it.

cheers,
   axel.

> Sincerely,
> Adrienne LaFleur
>
>
>
>
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-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.