[gmx-users] PSF files from .top to .psf

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 29 01:22:24 CEST 2011

On 29/03/2011 4:06 AM, Donovan B.T. wrote:
> Hi All
> I'm trying to measure some dipole moments in VMD using "measure dipole", 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 [by 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.

grompp -pp can write a post-processed .top file that does not have any 
#include statements. Hopefully that is suitable for top2psf.pl.


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