Dear Neha,
This topic was discussed in 2003/2004: you got a quite simple answer
for a complex problem (just my personal opinion)... The atomic charges
for L-amino-acid fragments were derived from L-dipeptides: This lead
to the Cornell et al. FF. The trick is that a L-dipeptide and a
D-dipeptide are enantiomers and both share identical charge values:
this is easy to check that by deriving charges for a first L-dipeptide
and then for the D- version by setting x -> -x.
No problem to report if oligo, poly-peptides and proteins are composed
of only L-amino-acids _OR_ only D-amino-acids: here one encounters
enantiomers (i.e. L vs D, or LL vs DD, or L...L vs D...D, etc...). On
the contrary a 'problem' could arise when inserting a D-amino-acid in
the middle of L-amino-acids: here diastereoisomers are generated and
diastereoisomers for sure share different charge values (DD vs LL =
enantiomers; DL vs LL or LDL vs LLL = diastereoisomers). So using a
force field that was developed for L-amino-acids/natural proteins and
their enantiomers is obviously correct; mixing D-amino-acids with
L-amino-acids leads to diastereoisomers and this is all but a trivial
problem...
If I remember correctly Dr Simmerling'group has published a paper
about this problem; I lost the reference of that paper...
regards, Francois
Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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 - 09:30:03 PDT
