Using impose command in tleap, I want to impose phi, psi torsion angles of a
protein which is 500 residues long, but it seems tleap can handle proteins with
only 248 residues.
Even if I am using sequence (and not imposing torsion angles) then also tleap is
not able to handle protein with more than 248 residues.
I am using following input file for tleap
input file for tleap (249 residues)
########################################################
source /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
input1=sequence { PRO VAL PHE ALA GLN GLN ASN TYR ALA ASN PRO ARG GLU ALA ASN
GLY ARG ILE VAL CYS ALA ASN CYS HIS LEU ALA GLN LYS ALA VAL GLU ILE GLU VAL PRO
GLN ALA VAL LEU PRO ASP THR VAL PHE GLU ALA VAL ILE GLU LEU PRO TYR ASP LYS GLN
VAL LYS GLN VAL LEU ALA ASN GLY LYS LYS GLY ASP LEU ASN VAL GLY MET VAL LEU ILE
LEU PRO GLU GLY PHE GLU LEU ALA PRO PRO ASP ARG VAL PRO ALA GLU ILE LYS GLU LYS
VAL GLY ASN LEU TYR TYR GLN PRO TYR SER PRO GLU GLN LYS ASN ILE LEU VAL VAL GLY
PRO VAL PRO GLY LYS LYS TYR SER GLU MET VAL VAL PRO ILE LEU SER PRO ASP PRO ALA
LYS ASN LYS ASN VAL SER TYR LEU LYS TYR PRO ILE TYR PHE GLY GLY GLN ARG GLY ARG
GLY GLN VAL TYR PRO ASP GLY LYS LYS SER ASN ASN THR ILE TYR ASN ALA SER ALA ALA
GLY LYS ILE VAL ALA ILE THR ALA LEU SER GLU LYS LYS GLY GLY PHE GLU VAL SER ILE
GLU LYS ALA ASN GLY GLU VAL VAL VAL ASP LYS ILE PRO ALA GLY PRO ASP LEU ILE VAL
LYS GLU GLY GLN THR VAL GLN ALA ASP GLN PRO LEU THR ASN ASN PRO ASN VAL GLY GLY
PHE GLY GLN ALA GLU THR GLU ILE VAL LEU GLN ASN PRO ALA }
savePdb input1 1e2vA.pdb
quit
########################################################
comand to execute tleap
/opt/softwares/amber11/exe/tleap -f inputfile
tleap output after executing it
########################################
-I: Adding /opt/softwares/amber9/dat/leap/prep to search path.
-I: Adding /opt/softwares/amber9/dat/leap/lib to search path.
-I: Adding /opt/softwares/amber9/dat/leap/parm to search path.
-I: Adding /opt/softwares/amber9/dat/leap/cmd to search path.
-f: Source 1e2vA.main.7531.input.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./1e2vA.main.7531.input
----- Source: /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
----- Source of /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB done Log file:
./leap.log
Loading parameters: /opt/softwares/amber9/dat/leap/parm/parm99.dat Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /opt/softwares/amber9/dat/leap/parm/frcmod.ff99SB Reading
force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/softwares/amber9/dat/leap/lib/all_nucleic94.lib Loading
library: /opt/softwares/amber9/dat/leap/lib/all_amino94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/all_aminoct94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/all_aminont94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/ions94.lib
Loading library: /opt/softwares/amber9/dat/leap/lib/solvents.lib
Segmentation fault
########################################
When I am using sequence length of 248 residues ( removing last ALA from
inputfile above) then pdb file is made but still "Segmentation fault" message
comes
input file for tleap (248 residues i.e. last ALA removed)
########################################################
source /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
input1=sequence { PRO VAL PHE ALA GLN GLN ASN TYR ALA ASN PRO ARG GLU ALA ASN
GLY ARG ILE VAL CYS ALA ASN CYS HIS LEU ALA GLN LYS ALA VAL GLU ILE GLU VAL PRO
GLN ALA VAL LEU PRO ASP THR VAL PHE GLU ALA VAL ILE GLU LEU PRO TYR ASP LYS GLN
VAL LYS GLN VAL LEU ALA ASN GLY LYS LYS GLY ASP LEU ASN VAL GLY MET VAL LEU ILE
LEU PRO GLU GLY PHE GLU LEU ALA PRO PRO ASP ARG VAL PRO ALA GLU ILE LYS GLU LYS
VAL GLY ASN LEU TYR TYR GLN PRO TYR SER PRO GLU GLN LYS ASN ILE LEU VAL VAL GLY
PRO VAL PRO GLY LYS LYS TYR SER GLU MET VAL VAL PRO ILE LEU SER PRO ASP PRO ALA
LYS ASN LYS ASN VAL SER TYR LEU LYS TYR PRO ILE TYR PHE GLY GLY GLN ARG GLY ARG
GLY GLN VAL TYR PRO ASP GLY LYS LYS SER ASN ASN THR ILE TYR ASN ALA SER ALA ALA
GLY LYS ILE VAL ALA ILE THR ALA LEU SER GLU LYS LYS GLY GLY PHE GLU VAL SER ILE
GLU LYS ALA ASN GLY GLU VAL VAL VAL ASP LYS ILE PRO ALA GLY PRO ASP LEU ILE VAL
LYS GLU GLY GLN THR VAL GLN ALA ASP GLN PRO LEU THR ASN ASN PRO ASN VAL GLY GLY
PHE GLY GLN ALA GLU THR GLU ILE VAL LEU GLN ASN PRO }
savePdb input1 1e2vA.pdb
quit
########################################################
log file for 248 residues input file
##############################################
-I: Adding /opt/softwares/amber9/dat/leap/prep to search path.
-I: Adding /opt/softwares/amber9/dat/leap/lib to search path.
-I: Adding /opt/softwares/amber9/dat/leap/parm to search path.
-I: Adding /opt/softwares/amber9/dat/leap/cmd to search path.
-f: Source 1e2vA.main.7531.input-1.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./1e2vA.main.7531.input-1
----- Source: /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
----- Source of /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB done Log file:
./leap.log
Loading parameters: /opt/softwares/amber9/dat/leap/parm/parm99.dat Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /opt/softwares/amber9/dat/leap/parm/frcmod.ff99SB Reading
force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/softwares/amber9/dat/leap/lib/all_nucleic94.lib Loading
library: /opt/softwares/amber9/dat/leap/lib/all_amino94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/all_aminoct94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/all_aminont94.lib Loading library:
/opt/softwares/amber9/dat/leap/lib/ions94.lib
Loading library: /opt/softwares/amber9/dat/leap/lib/solvents.lib
Writing pdb file: 1e2vA.pdb
Quit
Segmentation fault
###############################################
kindly help me to solve it, as many of my proteins are 500+ residues long
--
Sandeep Singh
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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Received on Tue May 14 2013 - 03:00:03 PDT
