[gmx-users] Re: Vacuum Simulations

Anton Feenstra feenstra at chem.vu.nl
Mon Feb 16 12:43:01 CET 2004

Martina Bertsch, PhD wrote:
> Could you give me the name of your script, or perhaps send it to me 
> along with some information on how to use it to convert an ffgmx itp 
> file to the ffG43a1 topology?

renumtop is one of the two you need. The way we do it here, and which works
fairly well, is the following:

1) use ProDrg to get a gromacs topology (with the Gromacs forcefield, ffgmx).
2) re-assign atom types. This you have to do manually, but it isn't too difficult.
    Having the Gromos manual handy helps, but most relevant information is also in
    the comments in the ffG43a* files (for atomtypes mainly in ffG43a1nb.itp).
3) use nr2nametop to change atom numbers to labels in your .top (or .itp) file.
    Now you can see atom names & types where the bonds, angles, dihs and idihs are
    defined in stead of just numbers. From this (and the info the comments in
    ffG43a1bon.itp) you must assign, again manually, bonded types to all interactions,
    i.e., one of the 'gb_*' for each bond, 'ga_*' for each angle, and so on.
4) finally, use renumtop to change labels back to atom numbers.

Possibly, you will have to assign or adjust charges, and of course you'll need
to check things carefully after building.

I attached both scripts (also renumtop, so you're sure you're not using an
outdated version).

P.S., I prefer to keep these discussions (also) on the list, so other people can
benefit from it (and it can be found back in the archives, as well)!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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 chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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