Re: [AMBER] How to turn H-bonding point charges

From: Matthew Guberman-Pfeffer <>
Date: Mon, 11 Oct 2021 12:23:41 -0400

Thanks Carlos for the quick response. I should have mentioned that I have no intention of running dynamics with H-bonds turned off. My idea is to remove those point charges from QM/MM calculations on MD snapshots. I’m trying to create an altered prmtop for use with the sander QM/MM interface in this post-processing sort of way.

It seems like I have to do the heavy lifting of identifying exactly which hydrogens I want to zero the charges on from the cpptraj H-bond analysis. If there’s any way to quickly extract the relevant information from the cpptraj H-bond output, I’d appreciate the tip.


> On Oct 11, 2021, at 10:18 AM, Carlos Simmerling <> wrote:
> *Message sent from a system outside of UConn.*
> 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 <
>> 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 - 09:30:02 PDT
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