Hello everyone
I am trying to simulate protein-ligand complex (my ligand is methyl-CoA)
but when i prepare ligand library i received following error:
rsiklinux1:~/amber12/bin # parmchk -i ligamc.mol2 -f mol2 -o ligamc.frcmod
drsiklinux1:~/amber12/bin # 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 ligamc.mol2
Loading Mol2 file: ./ligamc.mol2
Reading MOLECULE named UNK
/root/amber10/bin/tleap: line 8: 6008 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 $*
is this error because of my ligand (methyl-CoA) or some other issue
thanks for your help in advance
Sumra
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 25 2013 - 23:30:03 PDT
