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

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 29 01:26:09 CEST 2011

Mark Abraham wrote:
> 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.

I doubt it.  I wrote top2psf.pl to serve one very specific purpose - to convert 
MARTINI topologies into a useful .psf for one single moleculetype.  Even a 
concatenated topology with everything explicitly listed won't work.  People have 
tried it and emailed me wondering why it's not working.  Sorry, that's just not 
what it was designed to do.  Perhaps you can follow the logic of the script and 
design something more flexible for your needs.  The framework is there, but I 
have never had the need or desire to re-work it.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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