[gmx-users] Charge groups

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear All
> 
> Suppose I determined partial charges  on atoms of my molecules.
> How can I make charge groups of them?

Look for similar groups in the force field you're using, and refer to the 
Gromacs manual, section 4.6.2.

> For example I have a drug of 50 atom(of course along with it's hidrogenes),
> and all of my data for charges are as 1.3465728 (suppose they are 
> accurate and different to eachother)
> 

Sounds like a wildly inappropriate total charge.

> Is it possible to make charge groups with zero net charge?
> How?How can I learn these?
> Is there any server to do this for me?
> Thanks in advance for your guide.
> 
> 

Refer to the documentation of whatever program you're using to do these 
calculations.  Force field parameterization is hard; don't expect immediate 
success.  Even if you can get "sensible" charges, they still may not be 
sufficiently accurate within the guidelines of the chosen force field after 
you've done whatever validation is required.

-Justin

-- 
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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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