Re: [AMBER] Atom type parameterization and prmtop file

From: asdda asa <nadaafiva.gmail.com>
Date: Tue, 27 Jan 2015 10:15:55 +0800

Thanks so much Prof,
Here I attach the molecule.
Thanks in advance.

Sincerely,
nadaafiva

On Mon, Jan 26, 2015 at 10:34 AM, David A Case <case.biomaps.rutgers.edu>
wrote:

> On Mon, Jan 26, 2015, asdda asa wrote:
> >
> > I am confusing with atom types in my ligand. In the original journal of
> > Gaff (J Comput Chem 25: 1157, 2004), both cc—cc and cd—cd are assigned
> as
> > conjugated single bonds, and cc—cd is conjugated double bond. However in
> my
> > ligand which was aromatic with 18 pi electron, cc—cc was assigned as
> > conjugated double bonds, and cc—cd is conjugated single bond.
>
> It is certainly possible that antechamber is making a mistake with your
> particular ligand. Please double-check your reasoning, however, since
> alternate Lewis structures are often possible. If you wish, post the
> details
> of your molecule -- we can't say more without more information.
>
> > So, with these failure in the ligand parameterization, could I proceed to
> > the molecular dynamics simulation?
>
> I would certainly recommend doing a minimization using GAFF, and comparing
> that to a minimization with a quantum code, e.g. using DFT or MP2. A lot
> depends on what sort of simulation you are planning to do.
>
> >
> > My second question, how to use a tool like ParmEd or cpptraj to inspect
> the
> > prmtop file.
>
> (a) read section 13.2 of the manual (the chapter on ParmEd);
> (b) type "parmed.py" to start parmed, then type "help"
>
> ....dac
>
>
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Received on Mon Jan 26 2015 - 18:30:02 PST
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