Re: charge group

From: Josh Vermaas (
Date: Fri Mar 18 2016 - 11:36:21 CDT

There isn't a hard rule. For CHARMM, the first thing I'd do is run your
structure through CGenFF. Are the penalties high? If they aren't,
parameterization by analogy is defensible (probably), and due to its
expediency, its hard to argue against. If the penalties are high, you
get to parameterize it yourself. Which is hard. Hard enough that it will
suck up at least a month of your time and you still won't be sure if its
"right", because parameterization is *HARD*, and there is alot to learn.


On 03/18/2016 11:23 AM, faride badalkhani wrote:
> Thanks a lot dear Josh. I want to simulate a hyperbranched polymer and
> I have some problem with charge assignment. which one do you recommend:
> 1) performing ab initio calculations to find atomic charges or
> 2) using the atomic charges near to my structure from CHARMM 36
> topology file (I am using this FF)?
> Truly yours,
> Farideh
> On Fri, Mar 18, 2016 at 7:40 PM, Josh Vermaas <
> <>> wrote:
> Hi Farideh,
> Charge groups should be integers, and used to be mandatory before
> PME took care of long range electrostatics, since they were used
> to make sure that a dipole didn't get split across a
> cutoff-boundary. Now they are just nice to have, but I don't
> believe they are mandatory.
> -Josh Vermaas
> On 03/18/2016 10:56 AM, faride badalkhani wrote:
>> Dear all,
>> I need to know if it is mandatory to define charge groups in
>> residues?
>> and if it is, should total charge of each charge group be equal
>> to zero?
>> any help will be appreciated.
>> Truly yours,
>> Farideh

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