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 - 10:00:03 PDT
