[AMBER] RES: Incorrect ligand parameterization using GAFF

From: Emilia Pecora-de-barros <empecora.ucsd.edu>
Date: Fri, 14 Apr 2017 01:53:54 +0000

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 13 2017 - 19:00:04 PDT
Custom Search