[gmx-users] Charge groups in poly methyl methacrylic acid

Alex nedomacho at gmail.com
Wed Jun 6 06:04:20 CEST 2018

I would try to double-check with topology generators like 
http://erg.biophys.msu.ru/tpp/ on a short polymer chain (e.g. three 
links, termini passivated by H), or do a CHELPG calculation to look at 
the charge distribution within the central unit (OPLS and AMBER rely on 
CHELPG charges) to get an idea. That said, if the default linkage carbon 
(139) expects passivation, within a given unit you could simply set its 
charge to zero.

None of this sounds very robust, I know, but that's sort of the LEGO 
nature of OPLS.


On 6/5/2018 9:01 PM, Debadutta Prusty wrote:
> Hi everyone,
> I am new to gromacs and hence, this question might be naive. How does one
> go about assigning charge groups while creating new monomer topologies in
> .rtp files? What I gather from looking at similar posts is that the net
> charge of a charge group should be an integer (zero for a neutral group and
> positive/negative for charged groups). However, this rule does not seem to
> be that straight-forward in many cases. For a polymer PMAA  (
> https://en.wikipedia.org/wiki/Poly(methacrylic_acid)), the charged groups
> can be CO2H, CH3,CH2. According to opls fields, these groups have a net
> zero charge. However, the remaining carbon atom, which does not have a
> hydrogen, has a net charge of -0.02 if I use  opls_139 (C in alkane). Is
> there a way around this problem ?
> Thanks,
> Debadutta Prusty

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