Could you use an intermediate compound identical to your starting molecule
but with zero partial charges? Perturbing to that gives you electrostatic
contributions, then perturbing the intermediate to a dummy molecule gives
the vdw and cavity contribution. It may not be exactly what you want since
you also switch off (and on again in the vacuum step) the internal
electrostatics.
Kind Regards,
Thomas
On Wed, Oct 4, 2023 at 1:37 PM Xiaoyu Wang via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address (Xiaoyu Wang via AMBER ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Dear AMBER user,
>
> I am trying to set up a calculation on the evaporation free energy
> estimation. As I went through manual, I saw that AMBER implements the
> traditional soft-core potential for elec and vdw. But I did not find the
> section which describes the instruction to decouple elec and vdw
> separately. Can anyone guide me on this?
>
> Thanks in advance.
>
>
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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Oct 04 2023 - 05:30:02 PDT
