Ben Ahmady wrote:
Dear GROMACS users/developers
I've recently started a PhD and am currently looking at bilayer
formation of two-tailed alkyl phosphate esters. I've been using the
PRODRG server to generate topologies for use in GROMACS, and as per the
recommendations made in the paper by Lemkul et. al I have consistently
altered the charges/charge groups according to the charges reported in
similar molecules for which topologies are well established. However,
the "similar molecules" to which I'm referring to are phospholipids such
as DPPC rather than the alkyl phosphate esters in which I'm interested,
and as such I was concerned that the charges [for the alkyl phosphates]
I was implementing might not be entirely accurate. I therefore set about
rather ham-fistedly doing Bader analysis on the individual alkyl
phosphate molecules I'm studying to try to establish more realistic
charges to implement in the topology (more accurately: I ran the same
simulations concurrently with the established molecules like DPPC and
tried to find a relationship between their Bader charges and topologies
which I could use to make a realistic estimate of the charges on the
alkyl phosphate molecules).
I really have two questions and hoped that I might take the opportunity
to ask experienced users/scientists: the first is whether I'm wrong and
that in your opinion(s) it is in fact sensible to simply use the charges
from, say, DPPC in my alkyl phosphate molecules, and the second question
is - regardless of the answer to the first question - whether what I'm
doing is in your opinion(s) sensible. I hope these aren't inappropriate
questions.
Parameterization is a tough task, if done properly. If you find it came easy,
it's probably not right ;) It sounds like you're trying to work backwards from
PRODRG and correct the charges. While that can be OK, if you've committed to
using the Gromos96 force fields, I'd suggest you work the other way around.
Look into the literature and see if anyone else has done anything similar - what
force field did they use? Was it successful? Frankly, the details of
parameterization for Amber, CHARMM, and OPLS are significantly more detailed
than those of the Gromos96 force fields, so you may actually find it easier to
use the QM methods described for those other force fields.
The next most significant issue is validation. You have to have some criteria
by which your new parameters are judged. Again, this is a reason why Gromos96
can be tough, unless you have DeltaG of solvation for your compounds, or
suitable models thereof. There are alternatives, but they're not significantly
better. Reproducing some condensed-phase criteria is common to all the force
fields (some have additional QM geometry requirements).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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