Dear Amber users,
When I want to analyze hydrogen binds of a 30-mer DNA with ptraj I got the
following error:
ERROR in safe_malloc: Error in alloc of -2030981184 bytes
+++++++
.....
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> RMS to first frame using no mass weighting
Dumping RMSd vs. time (with time interval 1.00) to a file named rmsfirst.txt
Atom selection follows * (All atoms are selected)
7> ATOMICFLUCT: dumping atomic positional fluctuations by atom to file
fluctCA.txt
Atom selection [No atoms are selected]
7> AVERAGE: dumping the average of the coordinates to file average.pdb
start: 1 Stop [at final frame] Offset: 1
Atom selection * (All atoms are selected)
Output file information: File (average.pdb) is a PDB file
7> HBOND saved to series hbt,
data will be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.05
Estimated memory usage for this hbond call: 42.41 GB
donors: 953 acceptors: 3974 frames: 1000
7> HBOND saved to series time, output to file hb3_135,
data will not be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.00 angstroms, angle cutoff is 135.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 42.40 GB
donors: 953 acceptors: 3974 frames: 1000
7> HBOND saved to series time, output to file hb3_120,
data will not be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 42.40 GB
donors: 953 acceptors: 3974 frames: 1000
7> HBOND saved to series time, output to file hb3.5_120,
data will not be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 42.40 GB
donors: 953 acceptors: 3974 frames: 1000
7> HBOND saved to series time, output to file hb3.5_135,
data will not be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.50 angstroms, angle cutoff is 135.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.00
Estimated memory usage for this hbond call: 42.40 GB
donors: 953 acceptors: 3974 frames: 1000
Processing AMBER trajectory file /root/amber9/exe/DNA_nowat_md2.mdcrd
ERROR in safe_malloc: Error in alloc of -2030981184 bytes
++++++++++++++++++++++
I tried two ways:
1) applying a patch as Dan said:
http://archive.ambermd.org/201006/0200.html
but when I issued:
patch -p0 -N -r patch_rejects < ptraj_AT1.4_fixMaxFrames.patch
it got the following:
can't find file to patch at input line 16
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|Author: Daniel R. Roe
|Date: 2010-05-27
|Description:
|Fixes bug where ptraj actions would attempt to allocate a negative number
of
|bytes of memory when the number of frames to be read is unknown, i.e. file
is
|compressed or corrupted. The number of frames for compressed files can now
be
|calculated ahead of time. For gzip files this is simple, but for bzip2 and
|zip files this adds to the processing time since uncompressed file size
cannot
|be determined for these file types without external programs. For corrupted
|files the trajectory filesize is used to predict the number of frames.
|After applying the patch ptraj should be completely recompiled (i.e.
perform
|a make clean in the ptraj directory).
|-----------------------------------------------------------------------------
|--- AmberTools/src/ptraj/trajectory.h 2010-03-30 23:05:16.000000000 -0400
|+++ AmberTools/src/ptraj/trajectory.h 2010-05-27 11:16:27.928920475 -0400
--------------------------
File to patch:
what's the name of File to patch? I tried trajectory.h but It didn't work.
How can I perform a make clean in the ptraj directory?
2)
http://structbio.vanderbilt.edu/archives/amber-archive/2007/0279.php
I tried to modify the safe_malloc routine in
/src/ptraj/utility.c:
- safe_malloc(int size)
+ safe_malloc(size_t size)
But I didn't find "safe_malloc(int size)" to exchange it for
"safe_malloc(size_t size)"?
Can anyone help me?
Meanwhile:
# cat /proc/meminfo
MemTotal: 5054332 kB
SwapTotal: 32764556 kB
Regards,
Ehsan
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Received on Sat Sep 04 2010 - 09:30:03 PDT
