[gmx-users] pdb2gmx/prodrg

[David van der Spoel]

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
etc.

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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