[gmx-developers] Re: [gmx-users] Oh topology .. go away ...

Berk Hess gmx3 at hotmail.com
Wed Apr 10 12:39:33 CEST 2002

>From: Marc Baaden <baaden at smplinux.de>
>To: "Berk Hess" <gmx3 at hotmail.com>
>Subject: Re: [gmx-users] Oh topology .. go away ...
>Date: Fri, 05 Apr 2002 14:41:36 +0100
>although you are hopefully enjoying your holidays, I just wanted
>to let you know that we probably have found another problematic
>The scenario is:
>[ atomtypes ]
>[ nonbond_params ]    in ffXXXnb.itp
>[ atomtypes ]      in another itp included thereafter
>Changing a parameter in [nonbond_params] of ffXXXnb.itp does not
>affect the topology. Eg the second atomtypes seems to trigger
>generation of LJ pairs via the combination rule as well.

I thought this is what I told you, but correct me if I am wrong.
There are two problems:

1) You can not have type definitions after a [ moleculetype ] header,
   I added a check for this last week.

2) You should not have a [ atomtypes ] header after
   [ nonbonded_params ], since all the previous entries in
   [ nonbonded_params ] will be ignored.
   I'll try to fix this this week.

These are the only problems as far as I know.

>This affects eg methanol.itp, flexwat-ferguson.itp which come
>with the std Gromacs distribution.

This is very bad indeed. I can understand if somebody didn't program
a check for some incorrect input, but not checking if the standard
force-field files are correct is pretty bad.


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