[gmx-users] gromos96 forcefield

Kukol, Andreas a.kukol at herts.ac.uk
Fri May 9 15:00:45 CEST 2008


Check out ffG53a6.rtp (in gromacs/share/gromacs/top) for the atom name requirements for urea, the residue name is UREA. This and other files therein will also give you an idea how gromos96 files look like.

For the small alkane chain, you need to make an .itp file and include it in your topology. Read the manual and this:

http://wiki.gromacs.org/index.php/.top_file

Andreas

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Thomas Schlesier
> Sent: 09 May 2008 13:43
> To: gmx-users at gromacs.org
> Subject: [gmx-users] gromos96 forcefield
>
> dear all,
> till now i simulated with the gromos87 forcefield, but now i want to
> change it.
> i have two small molecules which consist of a short alkane chain and
> then an urea-group.
>
> i built my molecules with spartan and saved them as .pdb then i tried
> pdb2gmx, but this failed:
> Fatal error:
> Residue 'UNK' not found in residue topology database
> but i have no idea how i should name the residues so that they are found
> in the database.
> then i tried pdb2gmx with my .gro file (which i get from prodrg with the
> .pdb file), but here the same problem occured.
>
> the other thing that i tried was to make the files with the beta version
> of prodrg. i get the .gro/.g96 and .itp files but they look the same
> like the files for the gromos87 forcefield (different values but the
> same format).
> i used editconf on the .g96 file but it doesn't really work, the new
> .g96 file looks like:
>
> TITLE
>
> END
> POSITION
> END
> BOX
>    10.000000000   10.000000000   10.000000000
> END
>
> from that and the gromacs-user manual i get the idea that .gro and .96
> files use different formats, but i don't really know how the format for
> .g96 looks like (i looked for a user manual for gromos96, but didn't
> found one for free).
>
> so the question is:
> 1) is there a way to translate the gromos87 files to gromos96?
> or
> 2) what should i do with the files form prodrg beta that they work?
>
> thanks for an answer
> thomas
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