[gmx-developers] Amber force fields
lindahl at stanford.edu
Sat Jun 15 10:53:55 CEST 2002
I looked at the script Anton started writing, and there are a couple of
things I spotted:
* The default parameters in Amber are NOT sigma/epsilon, but rather
* Amber (and OPLS) uses a different version of the force constants in
field equations. This applies to both bonds and angles.
* Some of the newer dihedrals have more than one term, so we might as
well use R-B
* The dihedral definition isn't identical to gromacs for the normal
2-periodic proper. It
will differ by a factor of two if you just copy it.
In general, it's probably easier not writing very fancy scripts, since
most things need to
be checked carefully manually anyhow. I hacked up an extremely simple
translates the basic nonbonded and bonded interactions into Gromacs
format - you
can find it attached in a tarball together with the Amber parm99.dat and
output where I've added heavy hydrogen options and dummy constraints.
I won't put more work into Amber, but hopefully there are a couple of
you willing to continue
the work - it shouldn't be too difficult. What remains to be done:
* Double- & Triple-check things to make sure everything is correct this
far. There are
a couple of atoms (Fe,Cu) where Amber99 doesn't provide L-J
parameters, but you
might be able to find them in earlier versions, or just copy the OPLS
DO NOT try to understand the conversions from my script - derive them
yourself so we
are more confident if the two versions agree :-)
I did not divide the dihedral coefficients by the number of dihedrals
defined for a bond.
There is a coefficient for this in the Amber force field, but I don't
know if the recipe
says all dihedrals should be used or not. Check the literature.
* Write / edit the residue topology database. The only impropers you
need are those defined
in the OPLS rtp file, so just check that. For dihedrals I have no
idea if the default Gromacs
choices are fine, or if you need to define all dihedrals. Note that
there is a new option to the
rtp file (check ffoplsaa.rtp) so you can do this automatically
without any pdb2gmx options...
* Fix hydrogen & termini databases. This really needs to be automatic if
it should be part
of Gromacs. Sorry, but I don't consider it an acceptable solution to
edit each PDB file manually
and change the residue names ....
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