[Dock-fans] Error creating gaff.mol2
John J. Irwin
jji at cgl.ucsf.edu
Thu May 29 15:29:34 PDT 2008
hmmm. why not use convert.py from OEChem?
Teck Maan wrote:
> 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.
>
>
>
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
More information about the Dock-fans
mailing list