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.
Mark
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