[gmx-users] pdb2gmx/prodrg

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 9 10:32:40 CEST 2001

On Tue, 9 Oct 2001, Daan van Aalten wrote:

>Hi Anton
>Sure, but before that happens it needs to be tested a bit more. I haven;t
>actually heard of *anyone* (!) simulating a PRODRGged small molecule in
>GMX with success. That could mean lots of people have tried and it works
>perfectly or nobody has tried because it doesn;t work :-)
>(so if YOU out there have tried and failed/succeeded, let me know!)
>Once these small things work OK we can move onto entire proteins.
I think small molecules work (at least the ones I have seen).

If we are going to discuss future directions, this is what I would like:
- decoupling of topology and force field
- all topologies generated with all hydrogens
- get rid of atom numbers in topologies, use symbolic names throughout

This means topologies would be just a description of intermolecular
connections. I am quite sure that prodrg would do a good job here. Before
doing any calculations the topology (and coordinates) then should be
merged together with the force field of choice. This would probably be a
bit trickier, since not all force fields support all residues and atoms

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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