Just a minor addition to Jasons answer:
There is one type of MM parameter that is not irrelevant for the QM atoms:
the non-bonded van der Waals parameters. These are used for the van der
Waals interactions between MM and QM atoms.
For most purposes, the atomtyping done by antechamber should be sufficient.
--Marc
On 14 May 2014 12:29, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, 2014-05-14 at 15:00 +0400, James Starlight wrote:
> > More detaily:
> > firstly I've parametrized my chromophore (this pdb consisted of ALL
> > hydrohens included for first N and last C atoms) represented as the amino
> > acid
> > antechamber -i crq.mol2 -fi mol2 -o crq2.mol2 -fo mol2 -c bcc -s 2
> > parmchk -i crq.mol2 -f mol2 -o crq.frcmod
> >
> >
> > than I've made lib file using
> > source leaprc.ff99SB
> > source leaprc.gaff
> > crq = loadmol2 crq2.mol2
> > loadamberparams crq.frcmod
> > set crq head crq.1.N
> > set crq tail crq.1.C
> >
> > saveoff LIG ligand.lib
> >
> > doe such parametrization of non-standard residue correct in general?
>
> It depends on whether or not you are satisfied with the AM1-BCC charge
> derivation scheme. If you are satisfied, and parmchk does not yield any
> parameters that are zeroed with "ATTN" printed by them, then this
> process is sufficient.
>
> If you want more rigorous, reproducible charge derivation then you need
> to use some sort of multiconformational RESP fitting procedure (such as
> that automated by R.E.D. tools).
>
> Of course the statements above are intended to apply rather generally.
> If you _always_ plan on using QM to treat the entire CRQ residue, then
> the nature of the MM parameters (charges, parameters, etc.) are
> completely irrelevant and whatever helps you make a topology file is
> good enough.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed May 14 2014 - 05:30:02 PDT
