Dear Carlos,
Thank you. So is it better to use Amber ff14SB for the entire non-standard
residue to ensure consistency with the protein that it has been connected
with?
Also could I use RED program to generate parameters consistent with the
ff14SB force field?
Thanks in advance!
On Thu, Oct 27, 2016 at 7:38 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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--
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 - 11:00:02 PDT
