Hello Alexander,
This isn't an easy question to answer, and it depends a bit on what you
ligands are. However, in general the GAFF force field is designed to enable
people to model nonstandard residues, such as drug-like molecules. The LJ
parameters should be balanced with the other standard Amber force fields
(e.g. ff14SB). You will have to generate partial atomic charges on your own
(see R.E.D. or AM1-BCC). Using GAFF atom types will also keep your bonded
ligand parameters (and LJ too) from mixing with the protein bonded
parameters.
However, in some cases using existing protein parameters might(!) be
advantageous. An example of this would be when you have a natural product
that is composed of mostly amino acids.
Then you would figure out what parameters are missing due to the
nonstandard residues and optimize them to be compatible with the protein
force field.
In both cases, it would be best to try to validate your choices by
comparing to experimental data if you have it.
Bests,
K
On Tue, Mar 22, 2016 at 11:50 AM, alexander.zlobin <
alexander.zlobin.fbb.msu.ru> wrote:
> Hello, Amber community!
>
> Provided I have to prepare ligands for MD together with a protein, which
> force field is better to do parametrization of these ligands in: GAFF of
> some of Amber's 'ff..' fields, for instance 'ff14SB'?
>
> Thank you!
>
> __
>
> Sincerely yours,
> Alexander Zlobin
>
> School of bioengineering and bioinformatics,
> Moscow State University
>
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Received on Tue Mar 22 2016 - 05:00:04 PDT
