[gmx-users] MM dihedral scanning

[Mohsen Ramezanpour]

Dear Gromacs users,

For parameterization of a molecule in Charmm36, I have got the QM scanning
and partial charges from GAMMP server. However, the fitted parameters are
not good enough.
I decided to do the MM scanning and try to get better parameters for the
dihedral.

Unfortunately, I do not have any experience with this part, and I could not
find any tutorial for how to do this in Gromacs.
I was wondering if you are aware of any tutorial which could help me to
overcome this challenging step.

There are three parts of molecule which I am interested in its dihedral
parameters that I am stuck in it for a while:
1) (*2,2-Diethyl-1,3-dioxolane*)
http://www.chemspider.com/Chemical-Structure.217102.html?rid=378be046-1c14-4bce-ac46-6591776f7e08

dihedrals of O-C-CH2-CH3

2) (DIMETHYLPROPYLAMINE)
http://www.chemspider.com/Chemical-Structure.55178.html?rid=16e49844-d25d-48c8-b1b5-89fb2f9372bd

dihedral of CH3-N-CH2-CH2

Many thanks in advance for any suggestion.

Cheers
Mohsen

-- 
*Rewards work better than punishment ...*