The problem you will encounter is at the boundaries between gaff and
non-gaff atom types. For example, you need a bond parameter linking atoms
from 2 different models (gaff and ff14sb) , and it likely won't exist. The
same goes for using gaff on a whole residue that must be bonded to residues
that use other force fields. Currently gaff works well when interactions
between the 2 force fields are only between nonbonded interactions. If you
want to do what you propose, you will probably need to create a frcmod file
with all of the mixed terms for bonds, angles and dihedrals at the
interface. This can be done, but depending on what you are modeling it may
or may not already exist.
On Oct 27, 2016 12:21 PM, "Aditya G Rao" <aditya.grao.mail.huji.ac.il>
wrote:
Dear Amber users,
I'm trying to parameterise a non-standard residue. The residue is composed
of a cysteine and a tetrapyrrole bound to the sulphur of this cysteine.
My question is whether I can combine gaff2 and Amber (e.g. ff14sb)
parameters for this non-standard residue? I could use ff14SB for the
cysteine that is well parametrized and gaff2 for the tetrapyrrole. Is it
necessary to use only gaff2 or only Amber parameters for the whole residue?
Thanks in advance!
Aditya
--
Aditya G. Rao
PhD Student
Fritz Haber Research Center for Molecular Dynamics
Institute of Chemistry, HUJI
Givat Ram, Jerusalem, Israel
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Received on Thu Oct 27 2016 - 10:00:03 PDT
