On Wed, Mar 19, 2014 at 9:47 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
>
>
>
> 1) Is there any error in the making of topology and incrd files?
>
> 2) Is my charges are correct?
>
This is a loaded question, and I'm staying away from most of it. There is
no rigorous quantum-mechanical definition of a 'partial charge' (there's no
"partial charge" quantum operator), so any charge derivation strategy will
have pros and cons associated with it. bcc charges are commonly used, but
not necessarily universally reliable.
> 3) Later I want to mix this molecule into glycolipid. So do I need to
> incorporate the GLYCAM force fields in the making of topology and incrd of
> this molecule?
>
If you're simulating Lipids I'd suggest looking into the Lipid 14 force
field.
>
> 4) Can anyone give brief idea the importance of "improper torsion angles"?
>
Improper torsions are discussed in every major computational chemistry
textbook and googling "improper torsion" gives a ton of relevant sites to
look. Those are always better places to start than asking on a mailing
list.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 19 2014 - 09:30:03 PDT
