[gmx-users] Re Re Re: charge group in topology file

[Justin A. Lemkul]

alkasrivastava at iitb.ac.in wrote:
> Thanks for the reply
> 
> but if you see the charge group which include N and H is not an integer
> 
>      10   opls_238      2    ASN      N      3       -0.5    14.0067   ;
> qtot 0.5
>     11   opls_241      2    ASN      H      3        0.3      1.008   ;
> qtot 0.8
> 
> 
> 
> 
>     24   opls_238      3    ASN      N      9       -0.5    14.0067   ;
> qtot 0.5
>     25   opls_241      3    ASN      H      9        0.3      1.008   ;
> qtot 0.8
> 
> 
> so wherever NH charge group is the there the total charge is always fraction.
> Is is correct to continue with this.

It is not *always* true that a charge group will contain an integer charge, 
especially (as I have noticed) in using all-atom force fields (OPLS, AMBER, 
CHARMM).  As long as each residue, and thus your molecule as a whole, has an 
integer charge, then things are fine.

-Justin

> 
> Thanks
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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