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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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