[Dock-fans] Error creating gaff.mol2
Teck Maan
teck.m.lim at wmich.edu
Thu May 29 10:20:50 PDT 2008
Hi,
I made a ligand in chemdraw and would like to convert them into mol2
format using openbabel so that i could run a amber score on onto a pdb
file. But i run into this syntax error saying that (Multiple '.' in
NUMBER-like thing (5.1.gaff.mol2)). Below is the log.
log started: Thu May 29 13:14:34 2008
Log file: ./leap.log
> # LEaP called by /home/tkmaan/Desktop/dock6/bin/amberize_ligand
> source leaprc.gaff
----- Source: /home/tkmaan/Desktop/dock6/parameters/leap/cmd/leaprc.gaff
----- Source
of /home/tkmaan/Desktop/dock6/parameters/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Thu May 29 13:14:34 2008
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading
parameters: /home/tkmaan/Desktop/dock6/parameters/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
>
> # Begin DOCK Amber Score ligand specific processing
> frcmod=loadamberparams 5.1.frcmod
(Multiple '.' in NUMBER-like thing (5.1.frcmod))
Could not open file 5.1.frcmod: not found
> source leaprc.dock.user
-----
Source: /home/tkmaan/Desktop/dock6/parameters/leap/cmd/leaprc.dock.user
----- Source
of /home/tkmaan/Desktop/dock6/parameters/leap/cmd/leaprc.dock.user done
>> # DOCK Amber Score User Commands for LEaP
>> # This provides a hook into the amberization scripts.
>> # All these commands will be sourced by tleap in all the amberize
scripts.
>> # For example, one could define a new atom type and load its
parameters:
>> # This merely prevents unknown atom type and maybe hybridization
>> # comments from LEaP.
>> # addAtomTypes {
>> # { "Si" "Si" "sp3" }
>> # }
>> #
>> # Define the atom types and parameters for Tetrahedrally Bonded
Silicon.
>> # silicon = loadamberparams frcmod.dock.silicon
>>
>
> 5.1=loadmol2 5.1.gaff.mol2
ERROR: syntax error
(Multiple '.' in NUMBER-like thing (5.1.gaff.mol2))
> check 5.1
ERROR: syntax error
> savepdb 5.1 5.1.amber.pdb
ERROR: syntax error
(Multiple '.' in NUMBER-like thing (5.1.amber.pdb))
> saveamberparm 5.1 5.1.prmtop 5.1.inpcrd
ERROR: syntax error
(Multiple '.' in NUMBER-like thing (5.1.prmtop))
(Multiple '.' in NUMBER-like thing (5.1.inpcrd))
> quit
ERROR: syntax error
I am not sure where i am missing here. Below is the mol2 file i
generated from babel.
@<TRIPOS>MOLECULE
1-5.cdx
43 45 0 0 0
SMALL
GASTEIGER
Energy = 0
@<TRIPOS>ATOM
1 C 55.7772 -27.8227 0.0000 C.3 0 UNK0
0.0939
2 C 58.4083 -24.9006 0.0000 C.3 0 UNK0
0.0237
3 C 52.5960 -22.3127 0.0000 C.3 0 UNK0
0.1552
4 C 49.6739 -19.6816 0.0000 C.2 0 UNK0
0.2788
5 N 52.1850 -26.2234 0.0000 N.am 0 UNK0
-0.2715
6 O 50.4914 -15.8354 0.0000 O.2 0 UNK0
-0.2699
7 C 56.4422 -21.4952 0.0000 C.3 0 UNK0
0.0311
8 C 52.1850 -34.0877 0.0000 C.3 0 UNK0
0.0311
9 C 48.7796 -32.1216 0.0000 C.3 0 UNK0
0.1713
10 C 48.7796 -28.1894 0.0000 C.2 0 UNK0
0.2458
11 N 45.3743 -34.0877 0.0000 N.am 0 UNK0
-0.1964
12 O 45.3743 -26.2234 0.0000 O.2 0 UNK0
-0.2730
13 C 55.5903 -32.1216 0.0000 C.3 0 UNK0
0.0038
14 C 58.9957 -34.0877 0.0000 C.3 0 UNK0
0.0206
15 C 62.4010 -32.1216 0.0000 C.3 0 UNK0
0.1093
16 N 65.8064 -34.0877 0.0000 N.3 0 UNK0
-0.1314
17 C 38.5636 -38.0198 0.0000 C.3 3 UNK3
0.2109
18 CA 38.5636 -34.0877 0.0000 C.3 3 UNK3
0.1836
19 C 41.9689 -32.1216 0.0000 C.2 3 UNK3
0.2623
20 N 35.1582 -32.1216 0.0000 N.am 3 UNK3
-0.2949
21 O 41.9689 -28.1894 0.0000 O.2 3 UNK3
-0.2715
22 O 41.9689 -39.9859 0.0000 O.3 3 UNK3
-0.2180
23 CD 22.1242 -30.7988 0.0000 C.3 2 PRO2
0.0939
24 CG 24.0903 -27.3934 0.0000 C.3 2 PRO2
0.0237
25 CA 28.3475 -32.1216 0.0000 C.3 2 PRO2
0.1518
26 C 31.7529 -34.0877 0.0000 C.2 2 PRO2
0.2409
27 N 24.7553 -33.7210 0.0000 N.am 2 PRO2
-0.2718
28 O 31.7529 -38.0198 0.0000 O.2 2 PRO2
-0.2733
29 CB 27.9365 -28.2110 0.0000 C.3 2 PRO2
0.0310
30 CB 19.3805 -42.6285 0.0000 C.3 1 TYR1
0.0547
31 CA 20.1981 -38.7823 0.0000 C.3 1 TYR1
0.1721
32 C 23.9378 -37.5672 0.0000 C.2 1 TYR1
0.2437
33 N 17.2759 -36.1512 0.0000 N.3 1 TYR1
-0.1228
34 O 26.8600 -40.1983 0.0000 O.2 1 TYR1
-0.2733
35 CG 15.6408 -43.8436 0.0000 C.ar 1 TYR1
-0.0200
36 CD1 12.7187 -41.2125 0.0000 C.ar 1 TYR1
-0.0009
37 CE1 8.9790 -42.4276 0.0000 C.ar 1 TYR1
0.0417
38 CZ 8.1614 -46.2738 0.0000 C.ar 1 TYR1
0.1957
39 CE2 11.0836 -48.9050 0.0000 C.ar 1 TYR1
0.0417
40 CD2 14.8233 -47.6899 0.0000 C.ar 1 TYR1
-0.0009
41 OH 4.4217 -47.4889 0.0000 O.3 1 TYR1
-0.2866
42 H 35.1582 -28.1894 0.0000 H 3 UNK3
0.1499
43 N 45.9341 -20.8967 0.0000 N.am 0 UNK0
-0.0863
@<TRIPOS>BOND
1 1 5 1
2 1 2 1
3 2 7 1
4 3 5 1
5 3 4 1
6 3 7 1
7 4 43 am
8 4 6 2
9 10 5 am
10 8 9 1
11 8 13 1
12 9 11 1
13 9 10 1
14 10 12 2
15 11 19 am
16 13 14 1
17 14 15 1
18 15 16 1
19 17 18 1
20 17 22 1
21 18 20 1
22 18 19 1
23 19 21 2
24 42 20 1
25 20 26 am
26 23 27 1
27 23 24 1
28 24 29 1
29 25 27 1
30 25 26 1
31 25 29 1
32 26 28 2
33 32 27 am
34 30 31 1
35 30 35 1
36 31 32 1
37 31 33 1
38 32 34 2
39 35 36 ar
40 35 40 ar
41 36 37 ar
42 37 38 ar
43 38 39 ar
44 38 41 1
45 39 40 ar
Can somebody help? Thanks.
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