[gmx-users] regarding ligands in proteins

[Luke Czapla]

Hi,

  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
error).
  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?

regards,
Luke


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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>