[gmx-users] Charmm27 potential energies.

Eric Stokes ess13 at uw.edu
Thu May 9 22:33:54 CEST 2013


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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