Dear Ross
thank you for your suggestion .........
I will let you know whether it works or not
Regards
Sumra
On Mon, Nov 12, 2012 at 11:33 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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 |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
>
> 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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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Nov 11 2012 - 23:00:03 PST
