I have also added a Perl script to the GROMACS site (the VMD page):
http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD
The user provides an input topology file, and a .psf file is written, which can
be loaded as data for the structure in VMD. The !NBOND section seems to be the
most important in this regard, so the other sections are a bit rough, but it
seems to work alright.
The caveat is the topology must be one generated by MARTINI, in order to satisfy
all the pattern matching and the order of the topology. It should be fairly
easy to modify the program further to accommodate other layouts, but I haven't
had the need to do so.
-Justin
Nicolas Sapay wrote:
Hello Thomas,
I have a tcl script in my personal script library that might do what you
want to do. I didn't use it for quite a while, but it was working well
as far as I remember. I think it has been adapted from a script
available on the VMD website, but I don't remember exactly its history.
It doesn't seem too difficult to understand. You should be able to
modify it for your own purpose, if needed.
Cheers,
Nicolas
Thomas Schmidt a écrit :
Dear Omer,
many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)
Does anybody else have a solution (...to put GROMACS bond information
into VMD)?
Thomas
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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