Hi everybody,
I'm using Antechamber (AmberTools 14 including latest updates) as part
of a ligand preparation process required by Dock 3.7.
It's role is to convert mol2 input to mol2 output and setting correct
SYBYL atom types.
I noticed that bond types were incorrectly set in the output mol2,
however they look correct in the intermediate AC file.
The command used is
"antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -at sybyl"
The input mol2 file is this:
.<TRIPOS>MOLECULE
noname
18 18 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 O1 1.4153 4.7461 -0.6510 O.3 1 noname -0.3891
2 C1 2.1454 3.6875 -0.0278 C.3 1 noname 0.1178
3 C2 3.4517 3.5531 -0.7097 C.2 1 noname -0.0556
4 O2 3.8747 2.3922 -1.2691 O.3 1 noname -0.4696
5 O3 4.2182 4.5404 -0.7759 O.2 1 noname -0.4696
6 C3 1.3631 2.4148 -0.0093 C.2 1 noname -0.0429
7 C4 0.4743 2.0747 -1.0601 C.2 1 noname -0.0494
8 C5 -0.2204 0.8519 -1.0502 C.2 1 noname -0.0585
9 C6 -0.0354 -0.0527 0.0094 C.2 1 noname -0.0611
10 C7 0.8348 0.2697 1.0648 C.2 1 noname -0.0585
11 C8 1.5245 1.4967 1.0579 C.2 1 noname -0.0494
12 H1 1.0277 5.3081 0.0239 H 1 noname 0.2103
13 H2 2.3118 3.9694 1.0119 H 1 noname 0.0636
14 H3 0.3226 2.7652 -1.8898 H 1 noname 0.0626
15 H4 -0.9024 0.6051 -1.8639 H 1 noname 0.0622
16 H5 -0.5670 -1.0043 0.0126 H 1 noname 0.0622
17 H6 0.9747 -0.4311 1.8879 H 1 noname 0.0622
18 H7 2.1899 1.7381 1.8867 H 1 noname 0.0626
.<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 3 5 2
5 2 6 1
6 6 7 2
7 7 8 1
8 8 9 2
9 9 10 1
10 10 11 2
11 6 11 1
12 1 12 1
13 2 13 1
14 7 14 1
15 8 15 1
16 9 16 1
17 10 17 1
18 11 18 1
.<TRIPOS>SUBSTRUCTURE
1 noname 1
Note that atoms 3,4 and 5 together form a carboxylate group. In the
final output mol2 the bonds 3-4 and 3-5 are single bonds.
However, the intermediate ANTECHAMBER_*.AC files reveal that the atom
types (C.2 for atom 3 and O.co2 for atoms 4 and 5) and bond types (type
9, delocalized) are correctly set.
This seems to be a problem of antechamber when converting AC to mol2.
Can anyone reproduce this behaviour and/or has suggestions?
Thanks in advance,
Denis
--
D e n i s S c h m i d t
Graduate Student
Pharmaceutical Chemistry . Philipps-University Marburg, Germany
Tel +49 6421 28 21351
http://www.kolblab.org
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Received on Mon Dec 08 2014 - 07:30:04 PST
