Dr Walker,
We are trying to do an substrate-enzyme simulation. The substrate parameters
were found by a group that published their results. We asked them for the
parameters, and they sent the CHARMM topology and parameter files.
I've optimized the substrate and calculated the charges with Gamess (RHF,
6-31G), from that made a mol2 which antechamber was able to read and make a
frcmod using GAFF.
We'll have to closely compare the parameters and charges, and like you said,
make a decision about which to use.
Thanks,
David
On Mon, Aug 1, 2011 at 12:30 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > In that case I wont use all the parameters. I do not have CHARMM to
> > prepare
> > those files.
> >
> > However, I imagine that the atom charges are the same, regardless of
> > using
> > CHARMM or Amber. Is this so?
>
> Yes and no... The equation is the same so the charges will work. The
> philosophy in fitting those charges is slightly different. AMBER works on a
> per residue basis using a RESP procedure while CHARMM works on a group
> basis
> where each group must have an integer charge. e.g. methyl groups sum to
> zero
> charge. The electrostatic constant (the value of epsilon-R on the bottom of
> the direct space charge equation) is also slightly different in the two
> force fields. Couple with this the fact that things like the dihedrals are
> fitted specifically with the charge model in hand and you can see how
> complicated things become.
>
> That said, is all this lost in the noise? Probably... The question to ask
> is
> do you think you can defend your choice of parameters one way or the other.
> A simple question, I as a referee or examiner would ask is, you had an
> option to a) attempt to use the CHARMM parameters even though they aren't
> strictly compatible but will at least work to some degree vs b) taking the
> time to fit AMBER compatible parameters yourself. Why did you choose to a?
>
> There is no simple answer to this... It is the nature of research. But for
> example, if this was a residue on one side of the protein a long way from
> the active site that would be a reasonable defense in itself. There might
> be
> others such as a quick AM1-BCC resp fit showing almost no difference in the
> charges, or perhaps a previous publication that used the approach you did
> and showed that it did not make a difference, or maybe simulations of the
> ligand in question on it's own showing it matches experiment in one way or
> another etc etc.
>
> Maybe that is more info than you wanted but I hope it helps.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Mon Aug 01 2011 - 13:00:03 PDT
