Hello Pavan,
I do not know what version of NWChem you are using. NWChem at least version 4.5-4.7 does
not properly implement RESP, though it can give deceptively good-looking results on some
molecules. I will guess you want RESP, not plain ESP, as that's how AMBER charges were
assigned. NWChem is not suitable for RESP. I know that NWChem 5.0 has significantly
changed its RESP charge calculations, but they too were flawed (though in a different
way) when I used it in beta. If you want to verify that your software and methods are
reasonable, obtain the original RESP papers and confirm that you can reproduce results
for simple cases like butane and n-methylacetamide. NWChem seemed to give especially
unreasonable results on butane when I was doing my own verifications.
Residues in the AMBER force fields are, I believe, parameterized with multi-conformation
RESP. This is more complicated than vanilla RESP. Reproducing the standard residue
charges is hard. To assign charges, I suggest using GAMESS or Gaussian with RED II
(
http://www.u-picardie.fr/labo/lbpd/RED/). You will not exactly reproduce standard AMBER
values for nucleic acids or proteins, but the charges are reasonable and derived in a
nicely reproducible way.
Matt Ernst
> 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 - 06:07:33 PST
