AMBER Archive (2009)

Subject: [AMBER] help needed for HID

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Sun Jul 12 2009 - 13:16:08 CDT

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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