Dear Amber users,
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.
I'm thinking that the parameterization wasn't done properly, but the carbons involved in the double bond were correctly assigned as sp2. Does anyone have any input on what could be causing this pronounced flexibility and how I can fix this? Maybe the parameters for the dihedrals were not assigned correctly?
part of the mol2 file:
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
region of the frcmod file describing the dihedrals of interest:
DIHE
cc-ce-cd-cd 1 1.000 180.000 2.000 same as X -ce-ce-X
nd-cc-ce-cd 1 1.000 180.000 2.000 same as X -ce-ce-X
nd-cc-ce-ha 1 1.000 180.000 2.000 same as X -ce-ce-X
c -cc-ce-cd 1 1.000 180.000 2.000 same as X -ce-ce-X
c -cc-ce-ha 1 1.000 180.000 2.000 same as X -ce-ce-X
cd-cd-ce-ha 1 1.000 180.000 2.000 same as X -ce-ce-X
Best regards,
Emilia Pecora de Barros
PhD Student
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Received on Thu Apr 13 2017 - 10:30:03 PDT
