yes I agree- I don't know either. my point was just that it's probably not
work fixing that specific issue, since the conformational change ones are
the same since the change in chirality is bonds away from the side chains
that will interact differently. it would improve one part of your model,
but would leave all of the other problems that are of the same magnitude...
On Fri, Mar 13, 2015 at 1:51 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Carlos,
>
> > This is true in principle, but the amino acid charges were not developed
> > using oligos.
>
> Yes
>
> > The effects you mention could be true for any conformational
> > change and would need a polarizable model to do more accurately.
>
> This is well-known for conformations - this is far less obvious for
> diastereoisomers, which are 'potentially' different 'molecules' (they
> share different properties: NMR spectra, chromatography retention
> time, etc...). We had this same discussion in 2004 ;-)
>
> One could imagine designing different FF libraries for different
> diastereoisomers (for instance two different FF libraries for the DLD
> and a DDD tri-aminoacid fragments can be constructed with different
> charge values; different residue names can be used to differentiate
> them) while for sure different conformations of a given molecule share
> the same FF library! So conformations & enantiomers have to be treated
> 'the same way' i.e. with a common FF library, while diastereoisomers
> _can_ be differentiated without the introduction of a pol. force
> field: is it needed? Well, I do not know ;-)
>
> regards, Francois
>
>
> > 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?
> >>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 13 2015 - 11:30:04 PDT
