in parmed, you can select the atoms for the charge change based on name,
atom number and many other mask options. you would need to decide which
atoms to change.
be aware, however, that you cannot only disable hydrogen bonding since the
charge effects many other interactions as well (rotational barriers, etc).
It depends on which force fields you are using, but the typical ones such
as ff14SB and those dating all the way back to parm94 do not have a
specific term in the force field for hydrogen bonding.
On Mon, Oct 11, 2021 at 8:59 AM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Dear Amber Community,
>
> I want to test the impact of changes in H-bonding on the electrostatic
> potential felt by a cofactor. I know that the CHANGE command in ParmEd can
> be used to, for example, turn off the charges. But, what procedure can I
> use to turn off the charges for only hydrogens involved in H-bonding?
>
> Best,
> Matthew
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Received on Mon Oct 11 2021 - 07:30:02 PDT
