Hello,
You should apply all bug fixes. Extract a fresh copy of AmberTools 1.4 and
apply the bugfix.all file on ambermd.org/bugfixesat.html for AmberTools-1.4.
Good luck!
Jason
On Sat, Sep 4, 2010 at 12:23 PM, Ehsan Habibi <EHabibi.ibb.ut.ac.ir> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Sep 04 2010 - 13:30:03 PDT
