Re: partial charges for organic ligands

From: johan strumpfer (
Date: Sat Mar 26 2011 - 12:40:48 CDT

Hi Francesco,

It's not just about better approximating reality but also about using
the correct parameterisation procedure for consistency with what has
been done in the rest of the force-field. CHARMM uses a very specific
parametisation and hence AM1BCC charges may not be the best to use.
Aonther option would be to use the amber force field or generalised
amber force field with RESP charges.


On Sat, Mar 26, 2011 at 12:45 PM, Francesco Pietra
<> wrote:
> Hello:
> Is it any experience with partial charges of different origin for
> non-covalently-bound paired-electrons ligands of proteins (ff charmm
> with namd)? To minimize efforts (since I am not using paratool), I am
> starting with AM1-BCC partial charges for an ensemble in explicit
> membrane-water. The system reaches npt stability nicely. However, I
> wonder whether it is already known that other types of charges for the
> organic molecule may better approximate reality.
> thanks
> francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:50 CST