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?
>>
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Received on Fri Mar 13 2015 - 11:00:02 PDT
