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

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Mon Oct 19 16:53:47 CEST 2009

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.


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
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: coarse_grain.tcl
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091019/385b3174/attachment.ksh>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: nicolas_sapay.vcf
Type: text/x-vcard
Size: 390 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091019/385b3174/attachment.vcf>

More information about the gromacs.org_gmx-users mailing list