I have run ptraj cluster analysis on 1ns MD trajectory. Everything seemed fine
but the at the end
the following error message was thrown to the terminal. I could see all out put
files, successfully written,
but I am afraid because of these messages. Can someone please suggest me what is
going on?
---------------------------------------------------------------------------------------------------------------
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin ../b0101cxmd4.mdcrd
Checking coordinates: ../b0101cxmd4.mdcrd
Rank: 0 Atoms: 31851 FrameSize: 774005 TitleSize: 81 NumBox: 3 Seekable 1
PTRAJ: cluster out b0101md all amber representative pdb average pdb
averagelinkage sieve 5 clusters 4 rms mass ":25-28, 46-48, 93-97, 146-148,
161-162, 300"
MASK = :25-28, 46-48, 93-97, 146-148, 161-162, 300
Mask [:25-28, 46-48, 93-97, 146-148, 161-162, 300] represents 284 atoms
[No output trajectory specified (trajout)]
../b0101cxmd4.mdcrd: 5000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 5000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (../b0101cxmd4.mdcrd) is an AMBER trajectory (with box info) with 5000
sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> CLUSTERING.
Clusters will be assigned and output to files with the prefix "b0101md".
The clustering algorithm is AverageLink using RMS as the distance metric.
Cluster-to-cluster distance is measured by its centroid.
The cluster count is set to 4.
Clustering will be performed in two passes (sieve method).
Sieved frames in the first pass will be selected every 5 frames starting
from frame 1.
The atom selection for best fit is
:25-28,:46-48,:93-97,:146-148,:161,:162,:300
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 ../b0101cxmd4.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
The first pass through the trajectory is complete.
Read in the existing PairwiseDistances file
Clustering using the average linkage algorithm.
Aligning the most representative frames from each clusters to cluster 2.
Sieve was active. Preparing for the second pass.
Dumping out current clusters to file EndFirstPass.txt.
Clustering elapsed time: 86 seconds
Computing centroids and expanding clusters.
Ready for the second pass through the trajectories...
Processing AMBER trajectory file ../b0101cxmd4.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 5000 sets and processed 5000 sets.
Dumping accumulated results (if any)
PTRAJ CLUSTER: Clustering elapsed time: 516 seconds
Printing distribution of distances to file b0101md.txt
Distribution of Distances
[ 0.365, 0.424] -- 0.02% ( 87 out of 499500)
[ 0.424, 0.483] -- 0.28% ( 1374 out of 499500)
[ 0.483, 0.542] -- 1.64% ( 8186 out of 499500)
[ 0.542, 0.601] -- 5.12% ( 25596 out of 499500)
[ 0.601, 0.660] -- 10.27% ( 51277 out of 499500)
[ 0.660, 0.719] -- 14.25% ( 71200 out of 499500)
[ 0.719, 0.779] -- 14.71% ( 73459 out of 499500)
[ 0.779, 0.838] -- 13.14% ( 65642 out of 499500)
[ 0.838, 0.897] -- 11.77% ( 58778 out of 499500)
[ 0.897, 0.956] -- 9.94% ( 49669 out of 499500)
[ 0.956, 1.015] -- 7.46% ( 37284 out of 499500)
[ 1.015, 1.074] -- 5.11% ( 25543 out of 499500)
[ 1.074, 1.133] -- 3.15% ( 15741 out of 499500)
[ 1.133, 1.192] -- 1.76% ( 8802 out of 499500)
[ 1.192, 1.252] -- 0.84% ( 4188 out of 499500)
[ 1.252, 1.311] -- 0.36% ( 1818 out of 499500)
[ 1.311, 1.370] -- 0.12% ( 609 out of 499500)
[ 1.370, 1.429] -- 0.04% ( 194 out of 499500)
[ 1.429, 1.488] -- 0.01% ( 41 out of 499500)
[ 1.488, 1.547] -- 0.00% ( 12 out of 499500)
*** glibc detected *** ptraj: double free or corruption (!prev):
0x00000000127d99e0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3d53c71ce2]
/lib64/libc.so.6(cfree+0x8c)[0x3d53c7590c]
/lib64/libc.so.6(fclose+0x14b)[0x3d53c60d0b]
ptraj[0x4229e9]
ptraj[0x422ae2]
ptraj[0x422b08]
ptraj[0x449771]
ptraj[0x451f85]
ptraj[0x437cbf]
ptraj[0x4026da]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3d53c1d974]
ptraj[0x4022e9]
======= Memory map: ========
00400000-00557000 r-xp 00000000 00:1a 93135736
/home/tripos/amber11_install/amber11/bin/ptraj
00757000-00761000 rw-p 00157000 00:1a 93135736
/home/tripos/amber11_install/amber11/bin/ptraj
00761000-00765000 rw-p 00761000 00:00 0
11ae2000-130b3000 rw-p 11ae2000 00:00 0 [heap]
3d53800000-3d5381c000 r-xp 00000000 08:01 2148192
/lib64/ld-2.5.so
3d53a1b000-3d53a1c000 r--p 0001b000 08:01 2148192
/lib64/ld-2.5.so
3d53a1c000-3d53a1d000 rw-p 0001c000 08:01 2148192
/lib64/ld-2.5.so
3d53c00000-3d53d4c000 r-xp 00000000 08:01 2148193
/lib64/libc-2.5.so
3d53d4c000-3d53f4c000 ---p 0014c000 08:01 2148193
/lib64/libc-2.5.so
3d53f4c000-3d53f50000 r--p 0014c000 08:01 2148193
/lib64/libc-2.5.so
3d53f50000-3d53f51000 rw-p 00150000 08:01 2148193
/lib64/libc-2.5.so
3d53f51000-3d53f56000 rw-p 3d53f51000 00:00 0
3d55000000-3d55082000 r-xp 00000000 08:01 2147955
/lib64/libm-2.5.so
3d55082000-3d55281000 ---p 00082000 08:01 2147955
/lib64/libm-2.5.so
3d55281000-3d55282000 r--p 00081000 08:01 2147955
/lib64/libm-2.5.so
3d55282000-3d55283000 rw-p 00082000 08:01 2147955
/lib64/libm-2.5.so
3d55c00000-3d55c0d000 r-xp 00000000 08:01 2148203
/lib64/libgcc_s-4.1.2-20080825.so.1
3d55c0d000-3d55e0d000 ---p 0000d000 08:01 2148203
/lib64/libgcc_s-4.1.2-20080825.so.1
3d55e0d000-3d55e0e000 rw-p 0000d000 08:01 2148203
/lib64/libgcc_s-4.1.2-20080825.so.1
2b992e179000-2b992e17b000 rw-p 2b992e179000 00:00 0
2b992e185000-2b992e186000 rw-p 2b992e185000 00:00 0
2b992e186000-2b992e21c000 r-xp 00000000 08:01 3325914
/usr/lib64/libgfortran.so.1.0.0
2b992e21c000-2b992e41b000 ---p 00096000 08:01 3325914
/usr/lib64/libgfortran.so.1.0.0
2b992e41b000-2b992e41d000 rw-p 00095000 08:01 3325914
/usr/lib64/libgfortran.so.1.0.0
2b992e41d000-2b992ea54000 rw-p 2b992e41d000 00:00 0
2b9930000000-2b9930021000 rw-p 2b9930000000 00:00 0
2b9930021000-2b9934000000 ---p 2b9930021000 00:00 0
2b9945b7d000-2b9945f4f000 rw-p 2b9945b7d000 00:00 0
2b9945f50000-2b994647d000 rw-p 2b9945f50000 00:00 0
2b994647e000-2b99466b6000 rw-p 2b994647e000 00:00 0
7fff7c91b000-7fff7c930000 rw-p 7ffffffea000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
./as1.sh: line 2: 2629 Aborted
--------------------------------------------------------------------------------------------
thanks,
Senthil Natesan
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Received on Sun Oct 03 2010 - 10:30:04 PDT
