[gmx-users] itp file

[Anton Feenstra]

jozef hritz wrote:
> 
>         Dear Erik,
> I would like to ask again for force field parameters, because I don't
> have problem with some missing parameter, but I am not sure which
> parameters are taken in simulation. I have small ligand which contain also
> some atipical parts, e.g. 7-ring. In itp file I used for these carbons CR6
> or CB atom type and defined charges, all bond, angle and dihedral
> parameters. But during simulation lincs crash down and structure looks
> horrible. It is reason why I am asking when in top file are included
> ffgmx.itp (I need it for protein) as well as newmolecule.itp what
> parameters are taken in simulation e.g. for dihedrals and what
> parameters for L-J potential which are not in newmolecule.itp

I think the topology is processed sequentially, so if a certain 
interaction type is defined twice, the last one prevails. Contrary
to what Eric mentioned, I don't think there is a warning for re-
definition of an interaction type (but I'm not sure either).

A little while ago I wrote a small script that mimicks the processing
done by grompp, and produces a .top-like file with all parameters
filled in explicitly. I posted it to the list as an attachment named
'process_top'. You can use google search to find it:
1) go to www.google.com
2) type 'site:gromacs.org process_top' in the search field
3) hit enter

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "My Heart is Just a Muscle In a Cavity" (F. Black)        |
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