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

[Nicolas SAPAY]

> 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.

Thanks for posting the tcl script on the website, although this script has
been mainly coded by someone else. I have simply modified it for my own
purpose.

I also want to mention it is a good think to create a psf file if one work
with VMD. You store at once, bonds, atom types and charges. Actually, I
should have somewhere a .rtf file for the Martini amino acids and lipids
(the equivalent of the Gromacs rtp file for CHARMM). It can be used by
psfgen to generate a psf file with Martini bonds, charges and atom types.
If I can retrieve it in my archives, I will post it on the website.

Nicolas

>
> 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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