John wrote:
Hello,
I have run a few protein systems through simulations of varying lengths
and would like to find a way to visualize the trajectories. I have tried
to use the top2psf.pl <http://top2psf.pl> script to produce a usable
.psf file. I can get it to produce the .psf file, but am unable get VMD
to display anything for the trajectory other than a bunch of dots.
If you send me your input files (off-list) I will try to debug it. For most
simple cases, the script should produce usable output.
anyone had any luck displaying MARTINI trajectories with VMD and might
know where i am going wrong? any suggestions are very appreciated.
There's a Tcl script from the same site where you (presumably) found my script,
but I've never used it so I can't help you with that.
-Justin
-john
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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