Hello everyone,
I am trying to perform an AM1-BCC charge fit using antechamber. I am trying
to simulate paracetamol. To obtain an initial coordinate mol2 file, to use
for subsequent charge fitting, I used the ZINC database (as per suggested
via swissparm.ch). However, when the charges are fit using either
antechamber -i acet.mol2 -fi mol2 -o acet_bcc.mol2 -fo mol2 -nc 0 -c bcc -s
2
or
antechamber -i acet.mol2 -fi mol2 -o acet_bcc.mol2 -fo mol2 --c bcc -s 2
I obtain a paracetemol molecule whos net charge is -0.001 e. This seems
large to me. I intend to simulate upwards of ~2500 paracetemol molecules,
which would yield a net charge -2.5 e. I was wondering if someone could
comment on what would cause antechamber to not return a neutral molecule.
My initial guess was perhaps the initial configuration was poor, but given
that its from the ZINC database, I dont see how the initial configuration
could be that bad. Could someone please help? Here is my initial acet.mol2
file which I obtained from the ZINC database. Any help is greatly
appreciated.
.<TRIPOS>MOLECULE
ZINC18274777
20 20 0 0 0
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 C1 -2.1938 1.4701 0.6085 C.3 1 <0>
-0.1738
2 C2 -2.1691 -0.0367 0.6077 C.2 1 <0>
0.5100
3 O1 -3.0611 -0.6582 1.1456 O.2 1 <0>
-0.5253
4 N1 -1.1558 -0.6938 0.0094 N.am 1 <0>
-0.6760
5 C3 -1.0811 -2.0905 0.0916 C.ar 1 <0>
0.1315
6 C4 0.1554 -2.7160 0.1778 C.ar 1 <0>
-0.1278
7 C5 0.2283 -4.0925 0.2593 C.ar 1 <0>
-0.1267
8 C6 -0.9336 -4.8504 0.2546 C.ar 1 <0>
0.0907
9 C7 -2.1693 -4.2261 0.1680 C.ar 1 <0>
-0.1267
10 C8 -2.2439 -2.8493 0.0927 C.ar 1 <0>
-0.1043
11 O2 -0.8611 -6.2059 0.3344 O.3 1 <0>
-0.4991
12 H1 -3.0822 1.8186 1.1352 H 1 <0>
0.0977
13 H2 -1.3026 1.8478 1.1098 H 1 <0>
0.0926
14 H3 -2.2144 1.8337 -0.4188 H 1 <0>
0.0926
15 H4 -0.4783 -0.1997 -0.4782 H 1 <0>
0.4131
16 H5 1.0601 -2.1261 0.1808 H 1 <0>
0.1308
17 H6 1.1901 -4.5792 0.3264 H 1 <0>
0.1337
18 H7 -3.0735 -4.8168 0.1636 H 1 <0>
0.1330
19 H8 -3.2062 -2.3631 0.0301 H 1 <0>
0.1433
20 H9 -0.8763 -6.5480 1.2387 H 1 <0>
0.3908
.<TRIPOS>BOND
1 1 2 1
2 1 12 1
3 1 13 1
4 1 14 1
5 2 3 2
6 2 4 am
7 4 5 1
8 4 15 1
9 5 10 ar
10 5 6 ar
11 6 7 ar
12 6 16 1
13 7 8 ar
14 7 17 1
15 8 9 ar
16 8 11 1
17 9 10 ar
18 9 18 1
19 10 19 1
20 11 20 1
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
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Received on Tue May 03 2016 - 20:30:03 PDT
