> On Thu, Oct 10, 2013, mmalett.nmt.edu wrote:
>
>> Loading Mol2 file: ./PFB1.mol2
>> Reading MOLECULE named PFB
>> $AMBERHOME/bin/tleap: line 17: 20897 Segmentation fault (core
>> dumped)
>
> Can you post the PFB1.mol2 file (it doesn't seem to be in the tutorial you
> cite(?)) and the exact commands that preceded it (e.g. which leaprc file
> you
> used, etc.)
>
> The term "segmentation fault" by itself means nothing; we have to be able
> to
> reproduce the error in order to find out what is going on.
>
> ...thx...dac
>
the PFB1.mol2 file:
.<TRIPOS>MOLECULE
PFB
14 13 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 F 2.0650 -0.8980 1.1420 f 1 PFB -0.200800
2 C 1.9220 -0.1030 -0.0000 c3 1 PFB 0.609900
3 F1 2.9040 0.8940 0.0000 f 1 PFB -0.200800
4 F2 2.0650 -0.8980 -1.1420 f 1 PFB -0.200800
5 C1 0.5370 0.5450 -0.0000 c3 1 PFB 0.345600
6 F3 0.3940 1.3400 1.1420 f 1 PFB -0.176300
7 F4 0.3940 1.3400 -1.1420 f 1 PFB -0.176300
8 C2 -0.5370 -0.5450 0.0000 c3 1 PFB 0.345600
9 F5 -0.3940 -1.3400 -1.1420 f 1 PFB -0.176300
10 F6 -0.3940 -1.3400 1.1420 f 1 PFB -0.176300
11 C3 -1.9220 0.1030 0.0000 c3 1 PFB 0.609900
12 F7 -2.0650 0.8980 -1.1420 f 1 PFB -0.200800
13 F8 -2.9040 -0.8940 0.0000 f 1 PFB -0.200800
14 F9 -2.0650 0.8980 1.1420 f 1 PFB -0.200800
.<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 2 4 1
4 2 5 1
5 5 6 1
6 5 7 1
7 5 8 1
8 8 9 1
9 8 10 1
10 8 11 1
11 11 12 1
12 11 13 1
13 11 14 1
.<TRIPOS>SUBSTRUCTURE
1 1 TEMP 0 **** **** 0 ROOT
commands:
tleap -f leap_PFB.scrpt
leap_PFB.scrpt file:
source leaprc.gaff
PFB = loadmol2 PFB1.mol2
saveOff PFB PFB.lib
quit
Thank you for looking into this,
Michael Malett
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Received on Fri Oct 11 2013 - 09:30:04 PDT
