Hello all,
I am trying to reproduce the charges assigned to amino acids by AMBER. For
this I sequenced a 3aa (GLY VAL SER) protein using the sequence command in
xleap/tleap (ff02). I then took the coordinates of the atoms and used NWChem
[
http://www.emsl.pnl.gov/docs/nwchem/nwchem.html] to perform a HF/6-31G*
level of theory calculation to determine the ESP charges. Following are the
results:
---------------------------------------------X(6)-------Y(7)---Z(8)---NWCharges(9)--AMBERcharges(10)
ATOM 1 N GLY 1 -0.687 -5.818 0.297 -0.503335
0.1902
ATOM 2 H GLY 1 0.195 -5.665 0.764 0.343046
0.2056
ATOM 3 H GLY 1 -0.515 -6.314 -0.566 0.375220
0.2056
ATOM 4 H GLY 1 -1.350 -6.181 0.965 0.375253
0.2056
ATOM 5 C GLY 1 -1.214 -4.528 -0.103 0.142001 -
0.0766
ATOM 6 H GLY 1 -1.332 -4.503 -1.186 0.072779
0.0839
ATOM 7 H GLY 1 -2.182 -4.368 0.373 0.065774
0.0839
ATOM 8 C GLY 1 -0.265 -3.414 0.318 0.681102
0.6838
ATOM 9 O GLY 1 0.779 -3.676 0.910 -0.613077 -
0.5820
ATOM 10 N VAL 2 -0.632 -2.168 0.010 -0.706023 -
0.4938
ATOM 11 H VAL 2 -1.501 -2.007 -0.478 0.311659
0.3018
ATOM 12 C VAL 2 0.184 -1.022 0.355 0.374371 -
0.0530
ATOM 13 H VAL 2 0.311 -0.978 1.437 -0.053813
0.0393
ATOM 14 C VAL 2 1.561 -1.114 -0.293 0.431839
0.3674
ATOM 15 H VAL 2 2.065 -2.017 0.050 -0.072275 -
0.0145
ATOM 16 C VAL 2 1.407 -1.163 -1.810 -0.243063 -
0.3584
ATOM 17 H VAL 2 0.903 -0.260 -2.154 0.074711
0.0803
ATOM 18 H VAL 2 2.391 -1.228 -2.274 0.044719
0.0803
ATOM 19 H VAL 2 0.817 -2.036 -2.088 -0.010168
0.0803
ATOM 20 C VAL 2 2.388 0.108 0.094 -0.420366 -
0.3584
ATOM 21 H VAL 2 2.500 0.145 1.177 0.074288
0.0803
ATOM 22 H VAL 2 3.373 0.044 -0.370 0.072675
0.0803
ATOM 23 H VAL 2 1.885 1.012 -0.250 0.151211
0.0803
ATOM 24 C VAL 2 -0.465 0.273 -0.111 0.625491
0.6732
ATOM 25 O VAL 2 -1.544 0.254 -0.698 -0.651299 -
0.5855
ATOM 26 N SER 3 0.198 1.402 0.152 -0.742729 -
0.4421
ATOM 27 H SER 3 1.083 1.364 0.638 0.314861
0.2952
ATOM 28 C SER 3 -0.315 2.700 -0.240 0.449759 -
0.0356
ATOM 29 H SER 3 -0.431 2.733 -1.323 -0.046556
0.0666
ATOM 30 C SER 3 -1.670 2.973 0.405 0.343801
0.0748
ATOM 31 H SER 3 -2.381 2.209 0.092 -0.041351
0.0602
ATOM 32 H SER 3 -1.567 2.951 1.490 -0.068466
0.0602
ATOM 33 O SER 3 -2.141 4.259 -0.004 -0.718650 -
0.5420
ATOM 34 H SER 3 -2.994 4.432 0.402 0.398837
0.3718
ATOM 35 C SER 3 0.634 3.813 0.181 0.728715
0.5772
ATOM 36 O SER 3 1.679 3.552 0.773 -0.807708 -
0.7433
ATOM 37 O SER 3 0.366 4.987 -0.067 -0.753234 -
0.7433
Although the charges add up to 0 in both the cases, there are significant
differences in numbers and in some cases difference in the sign of charge.
Could somebody please explain where I've gone wrong and/or the proper way to
verify the charges produced by AMBER.
If I were to perform a similar analysis to a novel residue/drug using NWChem
Vs AMBER(antechamber), whose results should I use?
Thanks for your time.
Pavan
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Received on Sun Jan 21 2007 - 06:07:32 PST
