VMD-L Mailing List

From: Donovan B.T. (B.T.Donovan_at_soton.ac.uk)
Date: Mon Mar 28 2011 - 08:26:36 CDT

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
> >
> > 

--
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