[gmx-users] top2psf.pl issue: trying to use vmd w/ MARTINI protein

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 15 17:15:46 CET 2011

John wrote:
> Hello,
> While trying to visualize a MARTINI protein/trajectory in VMD, I came 
> across the script top2psf.pl <http://top2psf.pl>. i attempted to use it as:
>  > ./top2psf.pl <http://top2psf.pl> -i martini.top -o martini.psf
> this generates the error:
>  > Cannot open atoms for reading: No such file or directory
> Anyone encounter this or have any suggestions for visualizing MARTINI 
> proteins in VMD? Thank you for any help.

The required input is the actual protein topology (usually an #included .itp 
file within the .top).


> -j


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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