> On Fri, Oct 11, 2013, mmalett.nmt.edu wrote:
>> >
>> >> Loading Mol2 file: ./PFB1.mol2
>
>> .<TRIPOS>SUBSTRUCTURE
>> 1 1 TEMP 0 **** **** 0 ROOT
>
> The problem is with the above line, which is missing one of the needed
> elements. It should look like this:
>
> 1 PFB 1 TEMP 0 **** **** 0 ROOT
>
> The next question is: how did you create this mol2 file? If it came
> through
> the antechamber suite, we need to try to identify and trap the problem
> that
> led to not having the substructure name (second item in the line above).
>
> ....regards...dac
>
PFB1.pdb was created through JSME editor and converted from smiles format,
and ran through antechamber.
command used:
antechamber -i PFB1.pdb -fi pdb -o PFB1.mol2 -fo mol2 -c bcc -s 2
PFB1.pdb:
HEADER NONAME 27-Sep-13
NONE 1
TITLE
NONE 2
AUTHOR Apache
NONE 3
REVDAT 1 27-Sep-13 0
NONE 4
ATOM 1 F 0 2.065 -0.898 1.142 0.00 0.00
F+0
ATOM 2 C 0 1.922 -0.103 -0.000 0.00 0.00
C+0
ATOM 3 F 0 2.904 0.894 0.000 0.00 0.00
F+0
ATOM 4 F 0 2.065 -0.898 -1.142 0.00 0.00
F+0
ATOM 5 C 0 0.537 0.545 -0.000 0.00 0.00
C+0
ATOM 6 F 0 0.394 1.340 1.142 0.00 0.00
F+0
ATOM 7 F 0 0.394 1.340 -1.142 0.00 0.00
F+0
ATOM 8 C 0 -0.537 -0.545 0.000 0.00 0.00
C+0
ATOM 9 F 0 -0.394 -1.340 -1.142 0.00 0.00
F+0
ATOM 10 F 0 -0.394 -1.340 1.142 0.00 0.00
F+0
ATOM 11 C 0 -1.922 0.103 0.000 0.00 0.00
C+0
ATOM 12 F 0 -2.065 0.898 -1.142 0.00 0.00
F+0
ATOM 13 F 0 -2.904 -0.894 0.000 0.00 0.00
F+0
ATOM 14 F 0 -2.065 0.898 1.142 0.00 0.00
F+0
CONECT 1 2 0 0 0
NONE 19
CONECT 2 1 3 4 5
NONE 20
CONECT 3 2 0 0 0
NONE 21
CONECT 4 2 0 0 0
NONE 22
CONECT 5 2 6 7 8
NONE 23
CONECT 6 5 0 0 0
NONE 24
CONECT 7 5 0 0 0
NONE 25
CONECT 8 5 9 10 11
NONE 26
CONECT 9 8 0 0 0
NONE 27
CONECT 10 8 0 0 0
NONE 28
CONECT 11 8 12 13 14
NONE 29
CONECT 12 11 0 0 0
NONE 30
CONECT 13 11 0 0 0
NONE 31
CONECT 14 11 0 0 0
NONE 32
END
NONE 33
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Received on Fri Oct 11 2013 - 13:30:04 PDT
