[gmx-users] Charmm27 potential energies.

Dr. Vitaly Chaban vvchaban at gmail.com
Fri May 10 07:45:41 CEST 2013

The positive charge on the alpha-carbon should be expected. Many methods
(not only DFT) will predict tiny non-zero charges even on more remote
carbons, if you consider deprotonated form.

Protonated form is a neutral molecule. So, alpha -CH2- may be acceptably
described as having a a zero charge in total. You can distribute the +1e
charge throughout COOH (for instance, uniformly with respect to what you
have in COO(-)) to make it also neutral in total.

On a related note, it is not very time consuming to calculate electronic
structures of CH3-COOH(0e) and CH3-COO(-1e) and derive better electrostatic
charges for each site.

Dr. Vitaly Chaban

On Thu, May 9, 2013 at 11:33 PM, Eric Stokes <ess13 at uw.edu> wrote:

> Hello,
> I am attempting to generate force-field parameters for a fatty acid
> molecule that contains a carboxilic acid head group. I decided to use the
> parameters for stearic acid as the base for my molecule, since they contain
> similar structures with the only major change being a shorter hydrophobic
> tail. I noticed that the charge on stearic acid, and other molecules that
> have a carboxilic head group, is spread out with -0.9 residing on the head
> group and -0.1 on the second carbon. I need to use the protonated from of
> my molecule for my simulation, as well as the deprotonated form. I looked
> into the parameters for the COOH replacement in the Charmm27 force-field
> and used that to form the head group of the protonated form of my molecule.
> The problem that I am facing is that this left behind a charge of -0.1 that
> resides on the second carbon. Is there any way to find acceptable partial
> charges without doing the full Gaussian calculations? I would also
> appreciate it if someone could explain why the charges were split onto the
> second carbon in the first place.
> Thanks in advance,
> Eric Stokes
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