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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 9 Jul 2010 12:07:01 -0400

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



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


Received on Fri Jul 09 2010 - 09:30:02 PDT
Custom Search