Hi,
antechamber still ignores the net charge for the Gasteiger charge method.
It seems that Gasteiger charges can be computed for a non
neutral system. However, if we decide not to do that, we must
emit a loud message indicating that the net charge is being changed
to zero and document that feature.
Scott
Don't wait. The time will never be just right.
Napoleon Hill
On Tue, 26 Aug 2003, Junmei Wang wrote:
> It is a good suggestion for us to judge net charges of molecues with
> atomtype. I will check what tripos people did and design the defination
> file for atomtype.
>
> "Lee, Matthew"
>
> 08/26/2003 01:07 Subject
> PM AMBER: Antechamber formal charges
> with Gasteiger method
>
> In antechamber, the -c gas Gasteiger charge method does not seem to
> work correctly with the -nc arg set to a formal charge on molecules that
> have correct explicit protonation states. The charges produced still sum
> up
> to 0. (And btw, I did apply bugfix.17, which is not related to this
> problem.)
>
> Ultimately, it would be nice if antechamber's chemical perception
> engine could recognize that these oxygens are part of an acid and thus give
> this functional group a contribution of -1 to the total formal charge of
> the
> molecule. When Sybyl assigns Gasteiger charges on this same acid.mol2
> file,
> it does just that, correctly identifying this molecule has having a formal
> charge of -1, and assigning atomic charges that sum up to -1. I am unable
> to get antechamber to do just the latter part, after explicitly specifying
> a
> formal charge of -1 with "-nc -1".
>
> Below is a simple carboxylate acid.mol2 input file on which I used
> the following command and the output:
>
> antechamber -i acid.mol2 -fi mol2 -o acid_gstgr.mol2 -fo mol2 -nc -1 -c gas
> --------------------------------------------------
> .<TRIPOS>MOLECULE
> test_acid
> 13 12 1 0 0
> SMALL
> NO_CHARGES
>
>
> .<TRIPOS>ATOM
> 1 C1 24.6493 8.1810 33.0721 C.3 1 <1>
> 0.0000
> 2 H1 24.3127 8.1636 32.0250 H 1 <1>
> 0.0000
> 3 H2 23.8707 8.6387 33.7000 H 1 <1>
> 0.0000
> 4 H3 24.8383 7.1527 33.4138 H 1 <1>
> 0.0000
> 5 H4 26.3486 8.6326 31.0822 H 1 <1>
> 0.0000
> 6 H5 27.2324 9.9983 31.8441 H 1 <1>
> 0.0000
> 7 H6 25.4963 10.1775 31.4194 H 1 <1>
> 0.0000
> 8 O2 24.8248 10.0283 35.0474 O.co2 1 <1>
> 0.0000
> 9 C18 25.6482 10.1245 34.1051 C.2 1 <1>
> 0.0000
> 10 O3 26.2869 11.1915 33.9364 O.co2 1 <1>
> 0.0000
> 11 C19 25.8703 8.9564 33.1744 C.3 1 <1>
> 0.0000
> 12 C20 26.2651 9.4785 31.7804 C.3 1 <1>
> 0.0000
> 13 H20 26.6675 8.3277 33.5654 H 1 <1>
> 0.0000
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 11 1 1
> 4 1 4 1
> 5 12 5 1
> 6 12 6 1
> 7 12 7 1
> 8 8 9 ar
> 9 9 10 ar
> 10 9 11 1
> 11 11 12 1
> 12 11 13 1
> .<TRIPOS>SUBSTRUCTURE
> 1 **** 8 TEMP 0 **** **** 0 ROOT
> --------------------------------------------------
> Here are the atom records from the acid_gstgr.mol2 outupt file:
> .<TRIPOS>ATOM
> 1 C1 24.6490 8.1810 33.0720 c3 1 <1>
> -0.0521
> 2 H1 24.3130 8.1640 32.0250 hc 1 <1>
> 0.0239
> 3 H2 23.8710 8.6390 33.7000 hc 1 <1>
> 0.0239
> 4 H3 24.8380 7.1530 33.4140 hc 1 <1>
> 0.0239
> 5 H4 26.3490 8.6330 31.0820 hc 1 <1>
> 0.0239
> 6 H5 27.2320 9.9980 31.8440 hc 1 <1>
> 0.0239
> 7 H6 25.4960 10.1780 31.4190 hc 1 <1>
> 0.0239
> 8 O2 24.8250 10.0280 35.0470 o 1 <1>
> -0.2470
> 9 C18 25.6480 10.1240 34.1050 c 1 <1>
> 0.3577
> 10 O3 26.2870 11.1910 33.9360 o 1 <1>
> -0.2470
> 11 C19 25.8700 8.9560 33.1740 c3 1 <1>
> 0.0557
> 12 C20 26.2650 9.4790 31.7800 c3 1 <1>
> -0.0521
> 13 H20 26.6680 8.3280 33.5650 hc 1 <1>
> 0.0416
>
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Received on Sun Aug 05 2007 - 06:07:43 PDT
