Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption

From: <moitrayee.mbu.iisc.ernet.in>
Date: Fri, 9 Jul 2010 23:44:31 +0530 (IST)

Thanks a lot for your reply.
I am attaching two files ptraj.out and err.out.
Hope it is of help in tracing the problem.

I found something disturbing. In the ptraj.out file I found the clusters for
19900 sets whereas the run was for 2000 sets only.

 [ 0.599, 0.648] -- 0.11% ( 22 out of 19900)
  [ 0.648, 0.697] -- 0.56% ( 111 out of 19900)
  [ 0.697, 0.745] -- 1.35% ( 268 out of 19900)
  [ 0.745, 0.794] -- 2.82% ( 561 out of 19900)
  [ 0.794, 0.843] -- 5.49% ( 1092 out of 19900)
  [ 0.843, 0.892] -- 9.21% ( 1833 out of 19900)
  [ 0.892, 0.940] -- 13.55% ( 2697 out of 19900)
  [ 0.940, 0.989] -- 16.78% ( 3339 out of 19900)
  [ 0.989, 1.038] -- 16.05% ( 3194 out of 19900)
  [ 1.038, 1.086] -- 12.44% ( 2476 out of 19900)
  [ 1.086, 1.135] -- 9.17% ( 1824 out of 19900)
  [ 1.135, 1.184] -- 5.61% ( 1116 out of 19900)
  [ 1.184, 1.232] -- 3.24% ( 645 out of 19900)
  [ 1.232, 1.281] -- 1.74% ( 347 out of 19900)
  [ 1.281, 1.330] -- 0.89% ( 177 out of 19900)
  [ 1.330, 1.378] -- 0.52% ( 103 out of 19900)
  [ 1.378, 1.427] -- 0.27% ( 53 out of 19900)
  [ 1.427, 1.476] -- 0.12% ( 24 out of 19900)
  [ 1.476, 1.525] -- 0.06% ( 12 out of 19900)
  [ 1.525, 1.573] -- 0.03% ( 6 out of 19900)

Thanks once again. I would look forward to hear from you.

Regards,
Moitrayee


> I was unable to reproduce this error using the same command and a
> trajectory of 50000 frames (see attached output).
>
> Can you re-run ptraj with the same input, except at the top of your
> input file add the line "prnlev 5" (which enables some debugging
> info), and redirect both stdin and stderr to a file and send that to
> me? For example:
>
> ptraj.in:
> prnlev 5
> trajin trajectory.crd
> cluster out testcluster representative pdb average pdb averagelinkage
> clusters 12 rms sieve 10 .CA
>
> ptraj topfile ptraj.in > ptraj.out 2>&1
>
> Thanks!
>
> -Dan
>
> On Fri, Jul 9, 2010 at 8:12 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
>> Dear Amber Users,
>>
>> I am trying to do an averagelinkage clustering using ptraj cluster.
>> The scrpit for clustering is as follows:
>>
>> #!/bin/sh
>>
>> /soft/amber11/exe/ptraj 2zni.prm.top << EOF
>>
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11000_11010.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11010_11020.crd
>> ....
>> ...
>>
>> cluster out testcluster representative pdb \
>>   average pdb averagelinkage clusters 12 rms sieve 10 .CA
>>
>> Now when I use 11-12ns for clustering, the code work fine and I get the final
>> testcluster.txt output.
>> However, when I increase the no. of snapshots for clustering from 1000 to say
>> 1500/2000 and above, the second pass of the clustering stops with the
>> following
>> error:
>>
>> ******
>> PTRAJ CLUSTER:  Clustering elapsed time: 596 seconds
>>  Printing distribution of distances to file testcluster.txt
>>    Distribution of Distances
>>  [   0.599,   0.644] --   0.11% (    12 out of  11175)
>>  [   0.644,   0.688] --   0.46% (    51 out of  11175)
>>  [   0.688,   0.733] --   0.98% (   109 out of  11175)
>>  [   0.733,   0.777] --   2.09% (   234 out of  11175)
>>  [   0.777,   0.822] --   4.18% (   467 out of  11175)
>>  [   0.822,   0.866] --   7.52% (   840 out of  11175)
>>  [   0.866,   0.911] --  11.62% (  1298 out of  11175)
>>  [   0.911,   0.955] --  14.77% (  1650 out of  11175)
>>  [   0.955,   1.000] --  16.03% (  1791 out of  11175)
>>  [   1.000,   1.044] --  13.75% (  1537 out of  11175)
>>  [   1.044,   1.089] --  10.44% (  1167 out of  11175)
>>  [   1.089,   1.133] --   7.49% (   837 out of  11175)
>>  [   1.133,   1.178] --   4.76% (   532 out of  11175)
>>  [   1.178,   1.222] --   2.59% (   289 out of  11175)
>>  [   1.222,   1.267] --   1.57% (   176 out of  11175)
>>  [   1.267,   1.311] --   0.90% (   101 out of  11175)
>>  [   1.311,   1.356] --   0.33% (    37 out of  11175)
>>  [   1.356,   1.400] --   0.29% (    32 out of  11175)
>>  [   1.400,   1.445] --   0.09% (    10 out of  11175)
>>  [   1.445,   1.489] --   0.04% (     5 out of  11175)
>> *** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption
>> (!prev): 0x0000000002cbf500 ***
>> ======= Backtrace: =========
>> /lib64/libc.so.6[0x310aa70412]
>> /lib64/libc.so.6(cfree+0x8c)[0x310aa73b1c]
>> /lib64/libc.so.6(fclose+0x14b)[0x310aa5f1eb]
>> /soft/amber11/exe/ptraj[0x4248f9]
>> /soft/amber11/exe/ptraj[0x4249f2]
>> /soft/amber11/exe/ptraj[0x424a18]
>> /soft/amber11/exe/ptraj[0x44b15f]
>> /soft/amber11/exe/ptraj[0x4538b1]
>> /soft/amber11/exe/ptraj[0x4397fb]
>> /soft/amber11/exe/ptraj[0x4045ea]
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x310aa1dab4]
>> /soft/amber11/exe/ptraj(realloc+0x119)[0x4041f9]
>> ======= Memory map: ========
>> 00400000-00714000 r-xp 00000000 08:06 3240670
>> /soft/amber11/bin/ptraj
>> 00913000-0091d000 rwxp 00313000 08:06 3240670
>> /soft/amber11/bin/ptraj
>> 0091d000-04045000 rwxp 0091d000 00:00 0                                
>>  [heap]
>> 3109800000-310981a000 r-xp 00000000 08:03 554906
>> /lib64/ld-2.6.so
>> 3109a1a000-3109a1b000 r-xp 0001a000 08:03 554906
>> /lib64/ld-2.6.so
>> 3109a1b000-3109a1c000 rwxp 0001b000 08:03 554906
>> /lib64/ld-2.6.so
>> 310aa00000-310ab47000 r-xp 00000000 08:03 554908
>> /lib64/libc-2.6.so
>> 310ab47000-310ad47000 ---p 00147000 08:03 554908
>> /lib64/libc-2.6.so
>> 310ad47000-310ad4b000 r-xp 00147000 08:03 554908
>> /lib64/libc-2.6.so
>> 310ad4b000-310ad4c000 rwxp 0014b000 08:03 554908
>> /lib64/libc-2.6.so
>> 310ad4c000-310ad51000 rwxp 310ad4c000 00:00 0
>> 310ae00000-310ae82000 r-xp 00000000 08:03 555003
>> /lib64/libm-2.6.so
>> 310ae82000-310b081000 ---p 00082000 08:03 555003
>> /lib64/libm-2.6.so
>> 310b081000-310b082000 r-xp 00081000 08:03 555003
>> /lib64/libm-2.6.so
>> 310b082000-310b083000 rwxp 00082000 08:03 555003
>> /lib64/libm-2.6.so
>> 310b600000-310b615000 r-xp 00000000 08:03 554989
>> /lib64/libpthread-2.6.so
>> 310b615000-310b814000 ---p 00015000 08:03 554989
>> /lib64/libpthread-2.6.so
>> 310b814000-310b815000 r-xp 00014000 08:03 554989
>> /lib64/libpthread-2.6.so
>> 310b815000-310b816000 rwxp 00015000 08:03 554989
>> /lib64/libpthread-2.6.so
>> 310b816000-310b81a000 rwxp 310b816000 00:00 0
>> 3118800000-311880d000 r-xp 00000000 08:03 554965
>> /lib64/libgcc_s-4.1.2-20070925.so.1
>> 311880d000-3118a0d000 ---p 0000d000 08:03 554965
>> /lib64/libgcc_s-4.1.2-20070925.so.1
>> 3118a0d000-3118a0e000 rwxp 0000d000 08:03 554965
>> /lib64/libgcc_s-4.1.2-20070925.so.1
>> 2aaaaaaab000-2aaaaaaae000 rwxp 2aaaaaaab000 00:00 0
>> 2aaaaaac8000-2aaaaab5e000 r-xp 00000000 08:05 2715247
>> /usr/lib64/libgfortran.so.1.0.0
>> 2aaaaab5e000-2aaaaad5d000 ---p 00096000 08:05 2715247
>> /usr/lib64/libgfortran.so.1.0.0
>> 2aaaaad5d000-2aaaaad5f000 rwxp 00095000 08:05 2715247
>> /usr/lib64/libgfortran.so.1.0.0
>> 2aaaaad5f000-2aaaac26b000 rwxp 2aaaaad5f000 00:00 0
>> 2aaab0000000-2aaab0021000 rwxp 2aaab0000000 00:00 0
>> 2aaab0021000-2aaab4000000 ---p 2aaab0021000 00:00 0
>> 2aaad0513000-2aaad1ec6000 rwxp 2aaad0513000 00:00 0
>> 2aaad1ec7000-2aaad23ea000 rwxp 2aaad1ec7000 00:00 0
>> 2aaad23eb000-2aaad267c000 rwxp 2aaad23eb000 00:00 0
>> 2aaad267d000-2aaad290e000 rwxp 2aaad267d000 00:00 0
>> 7fff0c4bf000-7fff0c4d4000 rwxp 7ffffffea000 00:00 0                    
>>  [stack]
>> 7fff0c5fd000-7fff0c600000 r-xp 7fff0c5fd000 00:00 0                    
>>  [vdso]
>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                
>>  [vsyscall]
>> a2.sh: line 158: 23993 Aborted                 /soft/amber11/exe/ptraj
>> 2zni.prm.top  <<EOF
>>
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11000_11010.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11010_11020.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11020_11030.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11030_11040.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11040_11050.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11050_11060.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11060_11070.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11070_11080.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11080_11090.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11090_11100.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11100_11110.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11110_11120.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11120_11130.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11130_11140.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11140_11150.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11150_11160.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11160_11170.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11170_11180.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11180_11190.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11190_11200.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11200_11210.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11210_11220.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11220_11230.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11230_11240.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11240_11250.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11250_11260.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11260_11270.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11270_11280.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11280_11290.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11290_11300.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11300_11310.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11310_11320.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11320_11330.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11330_11340.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11340_11350.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11350_11360.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11360_11370.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11370_11380.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11380_11390.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11390_11400.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11400_11410.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11410_11420.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11420_11430.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11430_11440.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11440_11450.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11450_11460.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11460_11470.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11470_11480.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11480_11490.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11490_11500.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11500_11510.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11510_11520.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11520_11530.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11530_11540.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11540_11550.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11550_11560.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11560_11570.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11570_11580.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11580_11590.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11590_11600.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11600_11610.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11610_11620.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11620_11630.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11630_11640.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11640_11650.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11650_11660.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11660_11670.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11670_11680.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11680_11690.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11690_11700.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11700_11710.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11710_11720.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11720_11730.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11730_11740.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11740_11750.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11750_11760.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11760_11770.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11770_11780.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11780_11790.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11790_11800.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11800_11810.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11810_11820.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11820_11830.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11830_11840.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11840_11850.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11850_11860.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11860_11870.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11870_11880.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11880_11890.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11890_11900.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11900_11910.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11910_11920.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11920_11930.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11930_11940.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11940_11950.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11950_11960.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11960_11970.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11970_11980.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11980_11990.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.11990_12000.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12000_12010.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12010_12020.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12020_12030.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12030_12040.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12040_12050.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12050_12060.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12060_12070.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12070_12080.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12080_12090.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12090_12100.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12100_12110.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12110_12120.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12120_12130.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12130_12140.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12140_12150.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12150_12160.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12160_12170.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12170_12180.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12180_12190.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12190_12200.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12200_12210.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12210_12220.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12220_12230.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12230_12240.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12240_12250.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12250_12260.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12260_12270.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12270_12280.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12280_12290.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12290_12300.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12300_12310.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12310_12320.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12320_12330.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12330_12340.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12340_12350.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12350_12360.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12360_12370.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12370_12380.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12380_12390.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12390_12400.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12400_12410.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12410_12420.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12420_12430.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12430_12440.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12440_12450.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12450_12460.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12460_12470.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12470_12480.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12480_12490.crd
>> trajin /mnt/disk/rad_gyr_dhpylrs/sys2/CRD/2zni.12490_12500.crd
>>
>> cluster out testcluster representative pdb    average pdb averagelinkage
>> clusters 12 rms sieve 10 .CA
>>
>> EOF
>> ******
>>
>> Can you please tell me what is going wrong? I am using ambertools version 1.4
>> and during the "make test" there were no errors detected.
>>
>> Thanks a lot in advance.
>>
>> Sincere Regards,
>> Moitrayee
>>
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.




_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber




Received on Fri Jul 09 2010 - 11:30:03 PDT
Custom Search