[gmx-users] Non integer charge value

[Justin Lemkul]

On 5/11/18 6:20 AM, Hemalatha Jayabal wrote:
> I apologize for the previous formatting.

Well it's no better here but it's immediately clear you're still doing 
something wrong:

> [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> ; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
> 2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
> qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21

These charges are incorrect right off the bat. The [ PRO-NH2+ ] terminus 
has charges of -0.07 on N (with an atom type of NP), CA and CD are +0.16 
(types CP1 and CP3, respectively) and the two H atoms should have a 
charge of +0.24.

Without seeing what your full pdb2gmx command and screen output are, 
there's no way for any of us to know what you're doing incorrectly, but 
that's the source of the problem.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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