If I remember correctly the charges in the original paper were calculated
for two geometries for most of the residues.
I would suggest reading that paper (I don't know the reference, but it
should be easy to find it).
Marius
On Sun, Jul 12, 2009 at 8:16 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBER
>
> I was just testing the generation of partial charges of HID residue
> using RESP method. I capped HID with ACE on N-terminal and NME on
> C-terminal and optimized the molecule using
>
> #p HF/6-31G* gfinp gfprint geom=connectivity
>
> then generated the ESP by using:
>
> #p HF/6-31G* SCF=tight gfinp gfprint geom=connectivity pop=MK IOp(6/33=2)
>
> After that I followed RESP method (two steps) usnig resp program
> (Amber10). I found that there is a difference between my calculated
> charges and that inside xleap.
>
>
>
> atom amber charge my calculated charge
>
> N -0.4157 -0.320085
>
> CA 0.0188 0.026449
>
> C 0.5973 0.603543
>
> O -0.5679 -0.588240
>
> CB -0.0462 -0.242978
>
> CG -0.0266 -0.044801
>
> CD2 0.1292 0.112621
>
> NE2 -0.5727 -0.568863
>
> CE1 0.2057 0.181391
>
> ND1 -0.3811 -0.246646
>
> H 0.2719 0.227475
>
> HA 0.0881 0.093945
>
> HB2 0.0402 0.110400
>
> HB3 0.0402 0.110400
>
> HD1 0.3649 0.306931
>
> HD2 0.1147 0.109502
>
> HE1 0.1392 0.128956
>
>
>
> Sorry, does it make any sence? I know the charge can be changed by
> changing the molecular orientation, but a little bit, not like this.
>
> Any explanation please;
>
> thanks in advance;
> bill
>
>
>
>
>
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Received on Sun Jul 12 2009 - 18:07:40 PDT
