AMBER Archive (2008)

Subject: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ).

From: Lwin, ThuZar (ThuZar.Lwin_at_STJUDE.ORG)
Date: Fri Mar 14 2008 - 10:32:25 CDT

Hi all,
     I though I would repost the following again as I really need to know what problem I am having.

Hello Amber friends,

I am wondering how the charges for protonated histidine (HIP) are generated with tleap. After all, I checked charges of HIP in all_amino03.lib with those generated in the parm file(considering the conversion factor of 18.2223) and I found out that the charges are not the same. Here is how I processed tleap.

source leaprc.ff03
w = loadPdb file.pdb
saveAmberParm w file.parm file.rst

In the end of the leaprc.ff03 file, I have edited
# assumed that most often proteins use HIE

I have shown you bellow the side by side comparison of what I actually got in my parm file versus what is in the all_amino03.lib and what should have been in the parm file considering the conversion factor of 18.2223. Is there something that I am overlooking? Any help would be greatly appreciated.

charges in parm file HIP atom names charges in all_amino03.lib
                                                                   (in electron charge) (what's expected in parm file)
-2.74E+00 N -0.424967 -7.74388
3.19E+00 H 0.285872 5.209245
-2.54E+00 CA -0.375022 -6.83376
1.89E+00 HA 0.014621 0.266428
-1.93E+00 CB -0.332123 -6.05204
1.86E+00 HB2 0.107725 1.962997
1.86E+00 HB3 0.107725 1.962997
9.32E-01 CG 0.182399 3.323729
3.83E-02 ND1 0.087602 1.59631
4.71E+00 HD1 0.305096 5.559551
-6.07E-01 CD1 -0.013105 -0.2388
3.99E+00 HE1 0.230635 4.2027
-2.57E+00 NE2 -0.148766 -2.71086
6.44E+00 HE2 0.377295 6.875183
-2.62E+00 CD2 -0.192052 -3.49963
3.89E+00 HD2 0.235237 4.286559
1.23E+01 C 0.566646 10.32559
-9.88E+00 O -0.560417 -10.2121

Thu Zar

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