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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 21 00:59:11 CEST 2009

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.


> 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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