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

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 17 06:56:42 CET 2016

On 17/11/16 01:24, Mohsen Ramezanpour wrote:
> 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
> claim.
> 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
> dihedrals.
> 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
Why not use the official server
> Cheers
> Mohsen

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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