[gmx-users] regarding ligands in proteins

Luke Czapla czapla at rutchem.rutgers.edu
Wed Oct 24 21:03:09 CEST 2001

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
seemed more reasonable but still was not close to actual behavior.  I'm
going to be continuing looking at this but I really need some expert help
about how to interpret the force constants/charges given by PRODRG.


On Wed, 24 Oct 2001, David van der Spoel wrote:

> >Fatal error: Bond deviates more than half its own length
> This could be because you pasted them in the wrong place.
> But try renaming glucose first (be sure to take the right one!) and rerun
> pdb2gmx
> 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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