[MMTK] MInimization in MMTK using Amber

Andrei A. Korostelev korostel@chemmail.chem.fsu.edu
Wed, 03 Apr 2002 19:51:00 -0500


This e-mail will probably be best answered by Konrad while I would be 
grateful if there is a feedback from anyone else.

I try to energy minimize protein structures. In order to have some 
reference I compare the results to the Discover minimizations. Discover 
makes use of Amber as MMTK does. I hope there is no difference in 
minimization algorithms between Discover and MMTK. As a test I ran 
conjugate gradient of a distorted ala-gly dipeptide and both programs 
revealed the same structure.
Now I apply the same test to a little more complicated molecule. The 
difference between programs is significant now. So I wonder why there is 
a difference between two programs using the same force field?

Here is the set of more concrete questions:
1) Are there any distance cutoffs, switches (for electrostatics?) etc. 
in MMTK that would influence minimization?
2) Is it right that if I don't specify algorithm for electrostatics 
(Ewald etc.), MMTK uses Coulombic potential with constant (not 
distance-dependent) dielectric as a default?
3) How can I set and check a value for dielectric constant?
4) How can I check partial charges ascribed to each atom?

5) Would you recommend using MMTK2.2b instead of MMTK2.0 I'm using now? 
Where can I download 2.2b version (link to 
ftp://dirac.cnrs-orleans.fr/pub/MMTK/MMTK-2.2b1.tar.gz is not functional)?

Thanks,

Andrei.