Dear Amber users,
While I was running clustering algorithm "Cobweb" in ptraj, it finished unexpected with segmentation fault.
I believe there is no problem in the structure when I look at them.
Can anyone please tell me what I need to look at to track this problem?
The input shell script is like following.
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#!/bin/bash
#
#PBS -N ptraj
#PBS -j oe
#PBS -q serial_std
#PBS -l select=1:ncpus=1
export AMBERHOME=/work/apps/amber11
cd $PBS_O_WORKDIR
$AMBERHOME/exe/ptraj 1s3v_com.top << EOF
trajin 1s3v_tqd_now.trj 1 10000
cluster out 1s3v_tqd_now representative pdb average pdb all amber COBWEB clusters -1 verbose verb \
rms sieve 20 ":6-39,50-79,89-96,113-138,144-149,179-179,187-188"
EOF
------------------------------------------------------------------------------------------------------------------------------------------------
Then the results were like following:
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/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/work/apps/amber11/exe/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
VAL GLY SER LEU ASN CYS ILE VAL ALA VAL
SER GLN ASN MET GLY ILE GLY LYS ASN GLY
ASP LEU PRO TRP PRO PRO LEU ARG ASN GLU
PHE ARG TYR PHE GLN ARG MET THR THR THR
SER SER VAL GLU GLY LYS GLN ASN LEU VAL
ILE MET GLY LYS LYS THR TRP PHE SER ILE
PRO GLU LYS ASN ARG PRO LEU LYS GLY ARG
ILE ASN LEU VAL LEU SER ARG GLU LEU LYS
GLU PRO PRO GLN GLY ALA HIE PHE LEU SER
ARG SER LEU ASP ASP ALA LEU LYS LEU THR
GLU GLN PRO GLU LEU ALA ASN LYS VAL ASP
MET VAL TRP ILE VAL GLY GLY SER SER VAL
TYR LYS GLU ALA MET ASN HIE PRO GLY HIE
LEU LYS LEU PHE VAL THR ARG ILE MET GLN
ASP PHE GLU SER ASP THR PHE PHE PRO GLU
ILE ASP LEU GLU LYS TYR LYS LEU LEU PRO
GLU TYR PRO GLY VAL LEU SER ASP VAL GLN
GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU
VAL TYR GLU LYS ASN ASP NAP TQD
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin 1s3v_tqd_now.trj 1 10000
Checking coordinates: 1s3v_tqd_now.trj
WARNING in getArgumentDouble(): Scanning double precision argument failed
Rank: 0 Atoms: 3142 FrameSize: 76351 TitleSize: 30 NumBox: 0 Seekable 1
PTRAJ: cluster out 1s3v_tqd_now representative pdb average pdb all amber COBWEB clusters -1 verbose verb rms
sieve 20 ":6-39,50-79,89-96,113-138,144-149,179-179,187-188"
MASK = :6-39,50-79,89-96,113-138,144-149,179-179,187-188
Mask [:6-39,50-79,89-96,113-138,144-149,179-179,187-188] represents 1845 atoms
[No output trajectory specified (trajout)]
1s3v_tqd_now.trj: 10000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 10000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (1s3v_tqd_now.trj) is an AMBER trajectory with 10000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> CLUSTERING.
Clusters will be assigned and output to files with the prefix "1s3v_tqd_now".
The clustering algorithm is Cobweb(1), using XYZ coordinates as attributes.
The cluster count is set to -1.
Clustering will be performed in two passes (sieve method).
Sieved frames in the first pass will be selected every 20 frames starting from frame 1.
The atom selection for best fit is :6-39,:50-79,:89-96,:113-138,:144-149,:179,:187,:188
Output of type 'all' will be written to a file of type: 'Amber trajectory'
Output of type 'representative' will be written to a file of type: 'PDB'
Output of type 'average' will be written to a file of type: 'PDB'
Processing AMBER trajectory file 1s3v_tqd_now.trj
1% ............ 25% ............ 50% ............ 75% ............ 100% /var/spool/PBS/mom_priv/jobs/3690580.lapis.mssm.edu.SC: line 16: 12449 Segmentation fault $AMBERHOME/exe/ptraj 1s3v_com.top <<EOF
trajin 1s3v_tqd_now.trj 1 10000
cluster out 1s3v_tqd_now representative pdb average pdb all amber COBWEB clusters -1 verbose verb rms sieve 20 ":6-39,50-79,89-96,113-138,144-149,179-179,187-188"
EOF
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When I do the same clustering with the same protein but different ligand it worked fine.
Thanks in advances for any advices.
Best regards,
Seungyeul Yoo
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Received on Fri Nov 04 2011 - 12:30:04 PDT
