[MMTK] AMBER force field

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Wed, 26 Sep 2001 15:30:44 +0200

Hi all,

at the moment I am trying to write a modification AMBER parameter file
and I am running into problems. I have done the following: I have a
peptide ring consisting of glycine residues (so no termination) and have
defined an amino acid, analogous to glycine, but I have renamed the
AMBER atom types (e.g. C to WX, CT to WT) just to some made up names.
Then I tried to write a modification file for those atom types, and when
I set all parameters equal to the values of the original atom types, I
should get the same result for energy and minimization.
I did this by taking all parameters of the 'amber_parm94' file and
simply replacing names, i.e. C with WX, CT with WT and so forth. 

I compared the different energies by using 'universe.energyTerms()' and
all energies agree, except for the dihedral cosine sum. I also tried to
then remove all parameters from the file, where atom types not present
in glycine are in. This didn't change anything. 
Is there anything I have to be careful with dihedral terms in 
modification file? Maybe somebody has tried this before and could give
me a hint.

Another question: When I create the universe and specify the force field

is it possible to specify a modification file for AMBER? From how I
understood the code it should be something like
Amber94ForceField(modfile='amber_modfile'), is that right? Can I specify
the path and is the default path the one where 'amber_parm94' and
'amber_parm94.heme' are located?

Another thing: Is it possible to simulate a chain, e.g. consisting of
glycine residues in a periodic universe such, that the chain is repeated
in x-direction? I would create the chain with the options
'PeptideChain(n_terminus=0, c_terminus=0, circular=1)'. Is the bond
between the last residue in one unit cell and the first residue of its
repetition formed correctly, i.e. as a bond with the smallest possible


Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399