Dear Anshul,
Can you post your input file as an attachment please so that we can check it
for mistakes etc. The fact that running each of the commands in the input
file separately works suggests that there may be something slightly
different between your input file and the commands you manually type.
You should also try applying all of the leap bugfixes from
http://amber.scripps.edu/bugfixes60.html
Namely bugfixes: 8, 9, & 21
You are also using Amber6 which is considerably out of date now. Do you have
a newer version of amber you could try? Does the same thing still happen?
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of anshul.imtech.res.in
> Sent: 08 July 2004 14:41
> To: amber mail reflector
> Subject: AMBER: segmentation fault in leap
>
> 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 - 18:53:00 PDT
