[gmx-users] regarding ligands in proteins

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 24 22:17:07 CEST 2001

On Wed, 24 Oct 2001, Luke Czapla wrote:

>Hi David and Daan,
>  I think the problem is the force constants given to us by PRODRG.  Maybe
>someone has an idea why this is the case, but the bond c1 values were off
>by a very large factor (about 1000) than ones that are in the sample itp
>files (Urea for instance).  I made them closer to those values and it
this is due to the different definition of the bond potential in gromos96
and gromos87 force field (what PRODRG generates when you select gromacs).
The conversion formulas are in the gromacs manual.

How about pdb2gmx-ing the renamed glucose molecule?

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

More information about the gromacs.org_gmx-users mailing list