Hi Sumra,
Could you please try downloading and installing a copy of AmberTools v12
and see if the problem still exists. There used to be some issues with
mol2 files in older version of leap that may have only been fixed in newer
versions of AMBER. You can download AmberTools 12 free of charge here:
http://ambermd.org/AmberTools-get.html
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
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On 11/11/12 10:15 PM, "Sumra Wajid Abbasi 30-FBAS/MSBI/F09"
<sumra.msbi30.iiu.edu.pk> wrote:
>Hello every one
>I am again and again receiving following error..i tried but couldnąt solve
>it..Please help me out..
>Regards
>drsiklinux1:~/amber10/exe # antechamber -i lig1.pdb -fi pdb -o lig1.mol2
>-fo mol2 -c bcc -s 2
>Running: /root/amber10/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0
>-o
>ANTECHAMBER_BOND_TYPE.AC -f ac
>
>
>
>Running: /root/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
>ANTECHAMBER_AC.AC -p gaff
>
>Total number of electrons: 178; net charge: 0
>
>Running: /root/amber10/bin/mopac.sh
>
>Running: /root/amber10/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o
>ANTECHAMBER_AM1BCC.AC -f ac -p /root/amber10/dat/antechamber/BCCPARM.DAT
>-s
>2 -j 1
>
>Running: /root/amber10/bin/atomtype -f ac -p bcc -o
>ANTECHAMBER_AM1BCC.AC-i
>ANTECHAMBER_AM1BCC_PRE.AC
>
>
>drsiklinux1:~/amber10/exe # parmchk -i lig1.mol2 -f mol2 -o lig1.frcmod
>drsiklinux1:~/amber10/exe # source leaprc.gaffSB
>bash: leaprc.gaffSB: No such file or directory
>drsiklinux1:~/amber10/exe # tleap
>-I: Adding /root/amber10/dat/leap/prep to search path.
>-I: Adding /root/amber10/dat/leap/lib to search path.
>-I: Adding /root/amber10/dat/leap/parm to search path.
>-I: Adding /root/amber10/dat/leap/cmd to search path.
>
>Welcome to LEaP!
>(no leaprc in search path)
>> source leaprc.ff99SB
>----- Source: /root/amber10/dat/leap/cmd/leaprc.ff99SB
>----- Source of /root/amber10/dat/leap/cmd/leaprc.ff99SB done
>Log file: ./leap.log
>Loading parameters: /root/amber10/dat/leap/parm/parm99.dat
>Reading title:
>PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
>incl.02/04/99
>Loading parameters: /root/amber10/dat/leap/parm/frcmod.ff99SB
>Reading force field modification type file (frcmod)
>Reading title:
>Modification/update of parm99.dat (Hornak & Simmerling)
>Loading library: /root/amber10/dat/leap/lib/all_nucleic94.lib
>Loading library: /root/amber10/dat/leap/lib/all_amino94.lib
>Loading library: /root/amber10/dat/leap/lib/all_aminoct94.lib
>Loading library: /root/amber10/dat/leap/lib/all_aminont94.lib
>Loading library: /root/amber10/dat/leap/lib/ions94.lib
>Loading library: /root/amber10/dat/leap/lib/solvents.lib
>> source leaprc.gaff
>----- Source: /root/amber10/dat/leap/cmd/leaprc.gaff
>----- Source of /root/amber10/dat/leap/cmd/leaprc.gaff done
>Log file: ./leap.log
>Loading parameters: /root/amber10/dat/leap/parm/gaff.dat
>Reading title:
>AMBER General Force Field for organic mol., add. info. at the end (June,
>2003)
>> LIG=loadmol2 lig1.mol2
>Loading Mol2 file: ./lig1.mol2
>Reading MOLECULE named UNK
>/root/amber10/exe/tleap: line 8: 16053 Segmentation fault
>/root/amber10/bin/teLeap -I/root/amber10/dat/leap/prep
>-I/root/amber10/dat/leap/lib -I/root/amber10/dat/leap/parm
>-I/root/amber10/dat/leap/cmd $*
>drsiklinux1:~/amber10/exe #
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Received on Sun Nov 11 2012 - 23:00:02 PST
