[gmx-users] regarding ligands in proteins

Daan van Aalten dava at davapc1.bioch.dundee.ac.uk
Thu Oct 25 09:10:01 CEST 2001

Hi Luke

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:

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

More information about the gromacs.org_gmx-users mailing list