[gmx-users] generate topology file containing all parameters?

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 21 09:31:41 CEST 2006

David Mobley wrote:
> All,
> Is there any way to automatically generate a topology file containing
> all of the parameters that normally would come from the force field?
> For example, filling in each bond in the [ bonds ] section with
> explicit parameters that would instead usually come from the included
> force field file which has the [ bondtypes ] section?

short answer is No.
longer answer is, it could only be done in grompp, since pdb2gmx does 
not have the appropriate information.

I assume you would like to change stuff once you have it? For viewing 
purposes gmxdump -s gives you all information of course, but not so 
nicely presented.

> Thanks,
> David
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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