[gmx-users] molecule parameterization in charmm36 using GAAMP server

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Thu Nov 17 01:24:17 CET 2016

Dear Gromacs users,

I used GAAMP server to get the parameters for a small molecule (this is
part of a larger molecule).
This server optimizes the charges and all the soft dihedrals in an
iteration way (consistent with charmm36 and CGenFF philosophy). The output
files also include modified angle, bond, and all soft dihedral parameters.
This means, all the parameters are dependent to each other and I have to
use all of them together in my molecule. However, I am not sure about this

My question is then, weather or not it would be OK to ONLY pick the
parameters for "charges" and "ONE of those dihedrals" NOT the suggested
optimized parameters for atom types, angles, bonds, and other soft

This is because, when I made the initial .itp file for my molecule, I could
find bond, angles and soft dihedral parameters by analogy to existent
molecules in charmm36 ff. So, I want to trust on those analogy-based
parameters for now. The only parameters I was in doubt about were "charges"
and "one of those dihedrals".

Please let me know your opinion. Thanks in advance


*Rewards work better than punishment ...*

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