Justin A. Lemkul wrote:
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.
I added text to the above page describing both scripts, which are
attached. I'd have done that yesterday but the website was
intermittently down.
Mark
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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