VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 28 2011 - 15:52:54 CDT

Donovan,
  The PSF file format is very verbose. Every atom, bond, etc, is explicitly
specified, and there's no provision for replicating identical pieces of
substructure. If you load up a PDB file in VMD and then use the
AutoPSF plugin to generate a PSF file for it, you'll see what a more
complex example looks like. You can read the source code for the
VMD PSF reader/writer plugin here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/psfplugin_8c-source.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 28, 2011 at 02:26:36PM +0100, Donovan B.T. wrote:
> Hi All
>
> I've had a crack at this, but am having trouble with the .psf file format. I'm not sure that the conversion tool [top2psf] is coping with the .top file and its three .itn include files. I have tried numerous work around's for include files [but pulling them out into the .top file], but I cannot seem to find a way to get the .psf, .gro and .xtc formats all loaded correctly into VMD. Native conversion of the .top [includes extracted] into .psf doesn't work and nor does converting each .itp file individually and concatenating.
>
> The biggest hurdle is finding a suitable script for how I should format the .psf file, for example I have lipids and a solvent. Do I have to describe each and everyone of the lipids in the system and the same question to the solvent. Apologies for the ask, but I could find nothing other than quite simple molecules with no solvent as examples for .psf.
>
> Best wishes and thanks
>
>
> Brett
>
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Friday, March 25, 2011 2:11 PM
> To: Donovan B.T.
> Cc: Pawe? K?dzierski; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: measure dipole
>
> Hi,
> VMD doesn't compute partial charges, as these are normally
> provided by the force field your simulation is based on, and in most
> cases you would get the charge information into VMD by loading it from
> a file format that includes it. If you were using NAMD/CHARMM, that would
> be from a PSF file. I believe there was a script called "top2psf" for
> Gromacs that generates a PSF file from a .top file. I don't know how
> well it works, but it might give you the charge information that is
> not included in the XTC and GRO files.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 25, 2011 at 01:18:38PM +0000, Donovan B.T. wrote:
> > Hmm, I seem not be pulling out any charge information at all.
> >
> > >> set selatoms [atomselect top "name OW and (resid 129)"]
> > >> $selatoms get charge
> > 0.0
> >
> > This should be a oxygen atom on a water. There seem to be no partial charges at all. There are .gro and .xtc files [not my simulations] used to create the VMD render . Is VMD not computing the partial charges on the atoms??
> >
> > Thanks
> > ________________________________________
> > From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Pawe? K?dzierski [pawel.kedzierski_at_pwr.wroc.pl]
> > Sent: Friday, March 25, 2011 7:55 AM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: measure dipole
> >
> > On 24.03.2011 19:07, Donovan B.T. wrote:
> > > Getting measure dipole to work.
> > >
> > > I have a membrane system with water and I want to select a region and compute the dipole moment at that region. For a test case I tried just a single lipid, where this is selected as follows:
> > >
> > >
> > >>> set sel [atomselect top "resid 1"]
> > >>> $sel get name
> > >>>
> > > gives....
> > >
> > > C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 O17......etc etc
> > >
> > > now using
> > >
> > >>> measure dipole $sel
> > >>>
> > > 0.0 0.0 0.0
> > >
> > This may be too obvious, but have you checked this?:
> >
> > $sel get charge
> >
> >
> > > and does this no matter what the molecule is including water. I'm not getting any measured vector for the measured dipole. It's probably something simple. Am I doing this the best way? I'm using the whole molecule as a test initially.
> > >
> > > Thanks
> > >
> > >
>
> --
> 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 

-- 
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