[gmx-users] GAAMP parameterization

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Fri Apr 28 06:23:40 CEST 2017

Dear Gromacs users,

Using GAAMP server for parameterization, if the GAFF for
"initial parameters" is used instead of "CGenFF":

1) Can the results still be used for using simulation in "Charmm36" force
field? Assuming that all the other values are chosen as default ones in the
GAAMP webpage.

2) Will the result be the same (or approximately the same) with when
"CGenFF" is used as initial parameters?

3) Will the units for angles, dihedrals, distances, ... be in CGenFF or
GAFF? I was wondering if I can still use the cgen_charmm2gmx.py script for
conversions to use it in Gromacs package?

As I understood from the paper, GAAMP can give output for parameterization
in both Charmm and Amber force fields.

This could be easily tested by running the same job two times.
Unfortunately, GAAMP server has some problems at the moment so it will take
too much time to check this.

I appreciate your comments in advance.


*Rewards work better than punishment ...*

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