[gmx-users] Conversion of a Gromacs (sub)system to mol2 ?

Anton Feenstra feenstra at few.vu.nl
Mon Nov 29 17:49:00 CET 2004

Marc Baaden wrote:

> Hi,
> I would like to convert part of a simulation system (ATP to be exact)
> to the mol2 format to be able to feed it into another program requiring
> that input format.
> I have seen that there was a feed on the mailing list about eventual mol2
> support, but it is not quite clear to me whether anybody has given it a
> try.
> So what I'm asking for is whether there is any "working" pipeline to get
> from a gromacs system (eg PDB, GRO, ITP..) to a corresponding mol2 format.
> I have tried babel, which produces some mol2 file - in a black box way -
> which is not properly recognised by the program I want to work with.
> So I guess what I'd need is to be able to tell the converter some atom type
> correspondences.

Right - there is the catch. Basically, mol2 files are forcefield files
(although they are generally used as coordinate & topology files).
This means that writing .mol2 files from Gromacs entails an automated 
forcefield conversion - which IMHO should be distrusted at best - unless by 
chance you happen to have the pertinent forcefield native to mol2 files (is 
that Charmm?) in Gromacs as well...

Having said that, there is a workaround script (I called it 
'mergemol2+pdbtomol2' or something) I wrote that takes a 'template' mol2 
files and replaces its coordinates with that from a .pdb file. This allows 
you to do the 'Gromacs > mol2' conversion once (manually, or by e.g. babel, 
or most likely a combination), and then parse in any number of coordinate 
sets by doing e.g. 'mergemol2+pdbtomol2 template.mol2 coordinates.pdb > 

I don't have the script handy now, so please remind me tomorrow (European 
time) on my own mail adress (I sometimes skip reading the list ;-0 ) if you 
feel I may be forgetting about it...


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

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