Sorry, thank you.
On Tue, 24 Apr 2018, 02:12 David A Case, <david.case.rutgers.edu> wrote:
> 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 - 22:30:02 PDT
