[gmx-users] Coarse-Grain: GROMACS bond information to VMD

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 16:33:40 CEST 2009

I have also added a Perl script to the GROMACS site (the VMD page):


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.


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


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