[gmx-users] re: Phosphate esters

Ben Ahmady ahmady.ben at gmail.com
Tue Nov 1 20:07:56 CET 2011

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 

Many thanks

Ben Ahmady
EngD candidate
M3S Doctoral Training Centre
University College London

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