On Mon, Apr 23, 2018, roja rahmani wrote:
>
> I want to make .itp file for capped amino acids (with N-methylamid and
> acetyl group) compatible with GROMACS for AMBER-99 ff.
I suspect most people on the list are like me, and don't know what a
.itp file is....
> Is it possible to do it with antechamber DIRECTLY? or i should make some
> changes?
A capped amino acid in Amber would be represented as ACE-xxx-NME. You
could build the ones you want in tleap (or all of them) and look at the
charged you get. In this model, the xxx charges are independent of the
surroundings.
>
> Are these amino acid's charges extractable by optimization in gaussian
> (b3lyp/631g(p)) (mulikene charge),
You could "extract" such charges from a Gaussian calculation, but you
need to be very careful about what you do with them. If you want
charges that are compatible with the Amber94 charge model (which would
include the current ff14SB) this procedure would not work at all.
Consider just building the molecules in Amber, as disscussed above.
> how about connectivities? Are they reliable?
By "connectivities", do you mean bond lengths and force constants? Or
something else? B3LYP should give "reasonable" results. But above you
indicated a desire to have values "compatible" with Amber99. Extracting
information from DFT would not be the correct way to proceed for that
objective.
....dac
p.s.: it is generally polite to wait more than five hours before asking
the same question a second time.
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Received on Mon Apr 23 2018 - 15:00:03 PDT
