[gmx-users] regarding ligands in proteins
Daan van Aalten
dava at davapc1.bioch.dundee.ac.uk
Thu Oct 25 09:10:01 CEST 2001
The PRODRG server currently only writes a GROMACS topology suitable for the
forcefield. Other forcefield will NOT work as the force constants are
completely different (which explains the warnings you were receiving). If I
get some feedback from people succesfully using PRODRG topologies with GMX I
will also implement topology generation for the other force fields.
Luke Czapla wrote:
> 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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