Dear all,
when we run the tleap and source the input file, we faced the
followin problem
tleap
I: Adding /usr5/users/harpreet/amber6/dat to search path.
-I: Adding /usr5/users/harpreet/amber6/dat/leap/lib to search path.
-I: Adding /usr5/users/harpreet/amber6/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: /usr5/users/harpreet/amber6/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /usr5/users/harpreet/amber6/dat/parm94.dat
Loading library:
/usr5/users/harpreet/amber6/dat/leap/lib/all_nucleic94.lib
Loading library: /usr5/users/harpreet/amber6/dat/leap/lib/all_amino94.lib
Loading library:
/usr5/users/harpreet/amber6/dat/leap/lib/all_aminoct94.lib
Loading library:
/usr5/users/harpreet/amber6/dat/leap/lib/all_aminont94.lib
Loading library: /usr5/users/harpreet/amber6/dat/leap/lib/ions94.lib
Loading library: /usr5/users/harpreet/amber6/dat/leap/lib/water.lib
> source input78548.input2
----- Source: ./input78548.input2
----- Source of ./input78548.input2 done
ERROR: syntax error
Segmentation Fault (core dumped)
My input file uses the impose command to build the peptide from
its sequence. If we run all the tleap by giving all the commands in the
input file mannually then no problem occured.
input file is like this
peptide=sequnce{ LA HIS HIS HIS HIS HIS HIS GLY SER GLY LEU PHE ASP PHE
LEU LYS ARG LYS GLU VAL LYS GLU GLU GLU LYS ILE GLU ILE LEU SER LYS LYS PRO
ALA GLY LYS VAL VAL VAL GLU GLU VAL VAL ASN ILE MET GLY LYS ASP VAL ILE ILE GLY
THR VAL GLU SER GLY MET ILE GLY VAL GLY PHE LYS VAL LYS GLY PRO SER GLY ILE GLY
GLY ILE VAL ARG ILE GLU ARG ASN ARG GLU LYS VAL GLU PHE ALA ILE ALA GLY ASP ARG
ILE GLY ILE SER ILE GLU GLY LYS ILE GLY LYS VAL LYS LYS GLY ASP VAL LEU GLU ILE
TYR GLN }
impose peptide { 1 }{
{ N CA C N 179.96 }
{ C N CA C -180.0 }
}
impose peptide { 2 }{
{ N CA C N -180.0 }
{ C N CA C -180.0 }
{ N CA CB CG 60 }
{ CA CB CG ND1 94 }
}
impose peptide { 3 }{
similarly all the amino acids are imposed
Like This I am able to get the prmtop and crd files for the input
sequence.
Can anyone tell me where the mistake is?
Any advise is highly appreciated
with regards
Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352
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Received on Thu Jul 08 2004 - 12:53:01 PDT
