[gmx-users] Charmm27 potential energies.

Justin Lemkul jalemkul at vt.edu
Thu May 9 22:39:41 CEST 2013

On 5/9/13 4:33 PM, Eric Stokes 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.

Servers exist for this purpose, like SwissParam and ParamChem.  As for the 
charge assignments, you would have to investigate the primary literature source 
for those parameters and how they were fitted.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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