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 - 05:00:02 PDT
