[no subject]
Hi,
a few days ago, I asked for a program that could convert sybyl atom types to MM2
or other force-
fields for use in tinker. A. Stevens and C. Gonzalez suggested using the Babel
program.
I have tried babel-1.6. It can read sybyl mol2 fields and write MM2, MM3 and
tinker input files,
among other. However, I am not absolutely sure that the atom type conversion is
done adequately.
For instance, I have tried translating a mol2 file for a small molecule
(benz.mol2) to a tinker
file (benz.xyz) (files are at the end) The atom types generated for a tinker
output coincide with
those generated for MM2 and MM3, so i tried running tinker single-point energy
calculations using
the MM2, MM3 and tinker parameter sets. In all cases, tinker fails to calculate
the energy because
it finds bonds (and torsions) for which it has no parameters, e.g., for the MM2
force-field:
Undefined Bond Stretching Parameters :
Type Atom Names Atom Classes
Bond 1-C 7-C+ 2 30
Bond 7-C+ 8-N 30 9
Bond 7-C+ 9-N 30 9
Bond 8-N 15-H 9 23
etc.
It happens the same for most of the molecules I have tried. Anyone has had
similar problems ? Is
this actually a problem in the atom type translation or rather a limitation of
the MM2 force-field ?
(this molecule is actually [(C6H6)-C-(NH2)2]+)
Thanks.
--
Xavier Fradera
------------ (benz.mol2)
"at@at" <TRIPOS>MOLECULE
bezamidine
18 18 1 0 1
PROTEIN
GASTEIGER
INVALID_CHARGES
"at@at" <TRIPOS>DICT
PROTEIN protein
"at@at" <TRIPOS>ATOM
1 C1 6.2540 17.3460 23.1660 C.ar 1 BENZ1 0.0932
2 C2 5.9180 16.1210 22.5890 C.ar 1 BENZ1 -0.0269
3 C3 4.7620 16.0230 21.7990 C.ar 1 BENZ1 -0.0523
4 C4 3.9480 17.1560 21.6060 C.ar 1 BENZ1 -0.0554
5 C5 4.3030 18.3840 22.1750 C.ar 1 BENZ1 -0.0523
6 C6 5.4510 18.4930 22.9710 C.ar 1 BENZ1 -0.0269
7 C7 7.4670 17.4620 23.9910 C.cat 1 BENZ1 0.2620
8 N8 8.2990 16.3920 24.2200 N.pl3 1 BENZ1 -0.2466
9 N9 7.8230 18.6310 24.5880 N.pl3 1 BENZ1 -0.2466
10 H10 6.5450 15.2514 22.7496 H 1 BENZ1 0.0693
11 H11 4.4965 15.0781 21.3388 H 1 BENZ1 0.0653
12 H12 3.0431 17.0764 21.0145 H 1 BENZ1 0.0649
13 H13 3.6855 19.2573 21.9988 H 1 BENZ1 0.0653
14 H14 5.7182 19.4387 23.4285 H 1 BENZ1 0.0693
15 H15 9.1401 16.5092 24.8028 H 1 BENZ1 0.2545
16 H16 8.0813 15.4731 23.8088 H 1 BENZ1 0.2545
17 H17 7.2438 19.4728 24.4583 H 1 BENZ1 0.2545
18 H18 8.6718 18.6745 25.1698 H 1 BENZ1 0.2545
"at@at" <TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 1 7 1
4 2 3 ar
5 2 10 1
6 3 4 ar
7 3 11 1
8 4 5 ar
9 4 12 1
10 6 5 ar
11 5 13 1
12 6 14 1
13 7 8 1
14 7 9 1
15 8 15 1
16 8 16 1
17 9 17 1
18 9 18 1
"at@at" <TRIPOS>SUBSTRUCTURE
1 BENZ1 9 RESIDUE 1 I **** 0 ROOT
"at@at" <TRIPOS>SET
UNK_ATOMS STATIC ATOMS AMSOM **** Atom types guessed for these
atoms
9 1 2 3 4 5 6 7 8 9
------------ (benz.xyz)
18 bezamidine
1 C 6.254000 17.346000 23.166000 2 2 6 7
2 C 5.918000 16.121000 22.589000 2 1 3 10
3 C 4.762000 16.023000 21.799000 2 2 4 11
4 C 3.948000 17.156000 21.606000 2 3 5 12
5 C 4.303000 18.384000 22.175000 2 4 6 13
6 C 5.451000 18.493000 22.971000 2 1 5 14
7 C 7.467000 17.462000 23.991000 30 1 8 9
8 N 8.299000 16.392000 24.220000 9 7 15 16
9 N 7.823000 18.631000 24.588000 9 7 17 18
10 H 6.545000 15.251400 22.749600 5 2
11 H 4.496500 15.078100 21.338800 5 3
12 H 3.043100 17.076400 21.014500 5 4
13 H 3.685500 19.257300 21.998800 5 5
14 H 5.718200 19.438700 23.428500 5 6
15 H 9.140100 16.509200 24.802800 23 8
16 H 8.081300 15.473100 23.808800 23 8
17 H 7.243800 19.472800 24.458300 23 9
18 H 8.671800 18.674500 25.169800 23 9