This is true in principle, but the amino acid charges were not developed
using oligos. The effects you mention could be true for any conformational
change and would need a polarizable model to do more accurately.
On Mar 13, 2015 12:51 PM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
> Neha,
>
> > While I agree with Carlos simmerling's response regarding chirality of
> > amino-acids in a protein,
>
> You agree with "Carlos simmerling's response"? well, this is good ;-)
> my feeling is that this is just... a quite complex problem. Better
> reading papers about that to be aware of what's is going on and to
> clearly understand the approximations, which are applied...
>
> > I am not sure if this will apply to the polymer I
> > am simulating (previous RED mailing list). RED assigned same torsion
> angles
> > for both L- and D- isomers based on ff99Sb forcefield. Is it possible to
> > take chirality into account using RED or should I try changing the sign
> of
> > the dihedral N C *CA CB and N C *CA HA?
>
> changing the sign of the dihedral? I do not understand what you mean...
>
> 1) again two enantiomers share identical charge values; two
> diastereoisomers do not! Is the induced effect negligible? I would
> read papers about that to be at least aware of this problem...
>
> 2) Two enantiomers share identical FF parameters? again, yes; what
> about diasteresoisomers? Generally? well I have no idea; this is not a
> soup question ;-) For the amino-acid case, Yes, after approximation...
> ???
>
> 3) I think a FF library loaded in LEaP can be used for enantiomers and
> diastereoisomers as both are stereoisomers (same atomic
> connectivities). Better controlling what you do here. Obviously each
> amino-acid fragment has its FF library in the Amber FF...
>
> regards, Francois
>
>
> > ---------- Forwarded message ----------
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Date: 11 March 2015 at 21:55
> > Subject: Re: [AMBER] D- amino acids in ff10
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> > ff99SB and f14SB (preferred) were both designed and tested to work with D
> > amino acids without modification. There is no need to develop new
> > parameters or change inputs, as long as your coordinates are the D
> isomer.
> > I cannot say about other options.
> >
> > On Wed, Mar 11, 2015 at 9:45 AM, Neha Gandhi <n.gandhiau.gmail.com>
> wrote:
> >
> >> I am reiterating question which was posted several years ago regarding
> >> simulation of D-amino acids. I am trying to parameterise a molecule with
> >> D-Arginine side-chain with ff10. Do i need to change sign of the angles
> >> around C-alpha to take into account chirality?
>
>
>
>
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Received on Fri Mar 13 2015 - 10:30:02 PDT
