[gmx-users] topology

David spoel at xray.bmc.uu.se
Tue Nov 12 20:21:12 CET 2002

On Wed, 2002-11-13 at 03:11, Ruben Martinez Buey wrote:
> Hi everybody,
> How can I check if  a molecular topology (for GROMOS96) of a small
> molecule (a ligand of a protein) is OK??
> Are there another programs similar to PRODRG?? How can I check if the
> results of this program are OK??
> Thanks in advance
You may not like this, but especially for a small  molecules that are
non-standard you have to check manually whether the toplogy makes sense.
This is your research and you have to be able to explain why you have
used such and such parameters. 

Having said that the first test is to do an energy minimization or a
short simulation of the molecule in water, see if maintains the right
structure and has hydrogen bonds 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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