The results of changing the precision of the charge printout in sqm are
interesting.
Three decimals gives bad charges in the mol2 file. The charges do not
match the ones from the other precisions, and the difference from zero of
the total charge is in the 2nd digit, not the third.
Any precision above 3 that gives consistent charges with different
precisions that add to zero to the last digit.
*** I suggest we change the precision from f14.3 to f14.5 at least ****
>From antechamber, excerpt the atom lines for charges from sqm with
different formats.
f14.3
.<TRIPOS>ATOM
1 C1 3.1080 0.6530 -8.5260 c3 1 ETH
-0.094100
2 C2 4.5970 0.6740 -8.1320 c3 1 ETH
-0.094100
3 H11 2.8150 -0.3490 -8.7610 hc 1 ETH
0.031700
4 H12 2.5170 1.0150 -7.7110 hc 1 ETH
0.031700
5 H13 2.9560 1.2780 -9.3810 hc 1 ETH
0.031700
6 H21 4.7480 0.0490 -7.2770 hc 1 ETH
0.031700
7 H22 5.1870 0.3120 -8.9470 hc 1 ETH
0.031700
8 H23 4.8900 1.6760 -7.8970 hc 1 ETH
0.031700
f14.4
.<TRIPOS>ATOM
1 C1 3.1080 0.6530 -8.5260 c3 1 ETH
-0.093900
2 C2 4.5970 0.6740 -8.1320 c3 1 ETH
-0.093900
3 H11 2.8150 -0.3490 -8.7610 hc 1 ETH
0.031300
4 H12 2.5170 1.0150 -7.7110 hc 1 ETH
0.031300
5 H13 2.9560 1.2780 -9.3810 hc 1 ETH
0.031300
6 H21 4.7480 0.0490 -7.2770 hc 1 ETH
0.031300
7 H22 5.1870 0.3120 -8.9470 hc 1 ETH
0.031300
8 H23 4.8900 1.6760 -7.8970 hc 1 ETH
0.031300
f14.5
.<TRIPOS>ATOM
1 C1 3.1080 0.6530 -8.5260 c3 1 ETH
-0.093890
2 C2 4.5970 0.6740 -8.1320 c3 1 ETH
-0.093890
3 H11 2.8150 -0.3490 -8.7610 hc 1 ETH
0.031300
4 H12 2.5170 1.0150 -7.7110 hc 1 ETH
0.031300
5 H13 2.9560 1.2780 -9.3810 hc 1 ETH
0.031300
6 H21 4.7480 0.0490 -7.2770 hc 1 ETH
0.031300
7 H22 5.1870 0.3120 -8.9470 hc 1 ETH
0.031300
8 H23 4.8900 1.6760 -7.8970 hc 1 ETH
0.031300
f14.8
.<TRIPOS>ATOM
1 C1 3.1080 0.6530 -8.5260 c3 1 ETH
-0.093887
2 C2 4.5970 0.6740 -8.1320 c3 1 ETH
-0.093887
3 H11 2.8150 -0.3490 -8.7610 hc 1 ETH
0.031296
4 H12 2.5170 1.0150 -7.7110 hc 1 ETH
0.031296
5 H13 2.9560 1.2780 -9.3810 hc 1 ETH
0.031296
6 H21 4.7480 0.0490 -7.2770 hc 1 ETH
0.031296
7 H22 5.1870 0.3120 -8.9470 hc 1 ETH
0.031296
8 H23 4.8900 1.6760 -7.8970 hc 1 ETH
0.031296
--
Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887-0149 cell
On 2/1/12 11:28 AM, "David A Case" <case.biomaps.rutgers.edu> wrote:
>On Tue, Jan 31, 2012, Crowley, Michael wrote:
>
>> I wonder if there is something wrong with either my approach or with the
>> antechamber process.
>> Something as simple as ethane gives charges that do not add to zero
>> (+0.00200).
>
>The sqm program only prints Mulliken charges to three decimal places.
>Then
>when atom charges are symmetrized (so the equilvalent atoms have the same
>charge), round-off errors can accumulate.
>
>Try changing the qm2_print_charges.F90 file to print an extra digit of
>precision for the Mulliken charges. I'm guessing (hoping) that
>antechamber
>will pick that up, and you will get results closer to zero.
>
>....dac
>
>
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Received on Fri Feb 03 2012 - 12:00:02 PST
