I thought atom types ce and cc were sp2 carbons. Here is the entire mol2 file:
.<TRIPOS>MOLECULE
MOL
27 28 1 0 0
SMALL
resp
.<TRIPOS>ATOM
1 C1 0.3110 -1.0770 -0.0000 ce 1 MOL -0.020968
2 C2 1.5460 -0.4460 -0.0000 cc 1 MOL -0.011445
3 N1 1.8020 0.9340 -0.0000 nd 1 MOL -0.437192
4 C3 3.0970 1.0670 0.0000 cd 1 MOL 0.281771
5 C4 3.8170 2.3770 0.0000 c3 1 MOL -0.374587
6 N2 3.7720 -0.1490 0.0010 n 1 MOL 0.023771
7 C5 5.1900 -0.4020 -0.0000 c3 1 MOL -0.181880
8 C6 2.8040 -1.1850 0.0000 c 1 MOL 0.320529
9 O1 3.0830 -2.3900 -0.0000 o 1 MOL -0.592431
10 C7 -1.0040 -0.5650 -0.0000 cd 1 MOL -0.102540
11 C8 -1.3220 0.8310 -0.0000 cd 1 MOL -0.214415
12 C9 -2.6210 1.2440 -0.0000 cc 1 MOL 0.047418
13 F1 -2.8930 2.5780 -0.0000 f 1 MOL -0.220148
14 C10 -3.7880 0.3680 -0.0000 c 1 MOL 0.513667
15 O2 -4.9680 0.7690 0.0000 o 1 MOL -0.648964
16 C11 -3.3950 -1.0340 0.0000 cc 1 MOL 0.047418
17 C12 -2.1050 -1.4790 0.0000 cd 1 MOL -0.214415
18 F2 -4.4120 -1.9400 0.0000 f 1 MOL -0.220148
19 H1 0.3960 -2.1640 -0.0000 ha 1 MOL 0.111700
20 H2 3.0740 3.1780 0.0000 hc 1 MOL 0.108881
21 H3 4.4600 2.4950 -0.8830 hc 1 MOL 0.108881
22 H4 4.4600 2.4950 0.8840 hc 1 MOL 0.108881
23 H5 5.6830 0.0100 -0.8920 h1 1 MOL 0.076653
24 H6 5.6840 0.0100 0.8900 h1 1 MOL 0.076653
25 H7 5.3040 -1.4900 -0.0000 h1 1 MOL 0.076653
26 H8 -0.5180 1.5590 -0.0000 ha 1 MOL 0.168129
27 H9 -1.9200 -2.5500 0.0000 ha 1 MOL 0.168129
.<TRIPOS>BOND
1 1 2 1
2 1 10 2
3 1 19 1
4 2 3 2
5 2 8 1
6 3 4 1
7 4 5 1
8 4 6 2
9 5 20 1
10 5 21 1
11 5 22 1
12 6 7 1
13 6 8 1
14 7 23 1
15 7 24 1
16 7 25 1
17 8 9 2
18 10 11 1
19 10 17 1
20 11 12 2
21 11 26 1
22 12 13 1
23 12 14 1
24 14 15 2
25 14 16 1
26 16 17 2
27 16 18 1
28 17 27 1
.<TRIPOS>SUBSTRUCTURE
1 MOL 1 TEMP 0 **** **** 0 ROOT
________________________________________
De: David Case [david.case.rutgers.edu]
Enviado: quinta-feira, 13 de abril de 2017 22:40
Para: AMBER Mailing List
Assunto: Re: [AMBER] Incorrect ligand parameterization using GAFF
On Thu, Apr 13, 2017, Emilia Pecora-de-barros wrote:
>
> I'm trying to do ligand parameterization of a ligand of interest. I've
> done geometry optimization and RESP charge derivation using Gaussian
> 6-31G*, and parameters were derived using GAFF. However in the
> simulations this ligand is more flexible than expected, and even
> displays rotation of a double bond (between C1 and C2), going from a
> trans to cis conformation. The mol2 file generated is below.
Can you post the entire mol2 file, so that it can be easily visualized?
Antechamber is indeed assigning a single-bond to C1-C2 (atom types ce
and cc). There are certainly cases where the effective bond orders in
conjugated systems are not correct, and you may want/need to manually
modify either the atom types or the dihedrals involved.
....dac
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Received on Thu Apr 13 2017 - 19:00:04 PDT
