I am looking for a standalone application to perform geometry optimization on proteins and other macromolecules. It should support parameters for the AMBER force field (and probably others) and the possibility to add/modify those parameters. I will be using this app as part of a Python script to perform a lot of geometry optimizations. Tinker (http://dasher.wustl.edu/ffe/) could be a solution but have some drawbacks, 1) I can´t re-distribute the code 2) I would prefer to use pdb files directly (not to convert them to xyz files) 3) i would prefer to use amber parameters in this format http://ambermd.org/#ff
Thanks in advance.
Nop, I just want a geometry optimization routine that support the AMBER force field. I don´t want something that does what AMBER (the suite) does. AMBER, GROMACS NAMD etc are packages to perform molecular dynamics, MD involves a lot of different routines and geometry optimization is just a tiny subset of those routines. Probably I could take the GROMACS code and try to "isolate" the energy minimization routine, but I think it would be easier to start from some application smaller than GROMACS. I have been thinking on using Gabedit.
What about MMTK? It's in Python, free and open-source, and has the AMBER forcefield in it. I would still go with GROMACS though, it's small, fast, and easy to install.
http://dirac.cnrs-orleans.fr/MMTK/
I want to (eventually) re-distribute the code. It make not sense to make my code depends on whole gromacs if I only going to use the minimization routine. MMTK is an interesting workaround for my problem MMTK is very modular so it would be relatively easy to isolate the minimization routine.