[gmx-users] regarding ligands in proteins

Luke Czapla czapla at rutchem.rutgers.edu
Wed Oct 24 18:04:42 CEST 2001


  I would like to use that ffG43a1 force field (the Proteins only ffgmx
force field won't work with Calcium ions), so I would need suitable
replacements for CS1, OS, and HO (I don't know why using HO gives an
  I followed your advice about pasting the coordinates into the .GRO file.
However, when I go to run a position restraint or skip this to start the
MD simulation (this is after energy minimization which I believe had a
problem because the forces looked suspiciously high), I get this:
Fatal error: Bond deviates more than half its own length

And the problem atoms are all the atoms in Glucose.  Any ideas?


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

> CS1 is in the ffgmx force field, but for some reason not in the newer
> ffG43a1 force field. Don't know why.
> 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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