Re: [AMBER-Developers] final (!?!) release candidate for Amber11

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 16 Apr 2010 17:42:00 -0400

The weird behavior with the average command has to do with the new paradigm
of setting the trajectory stop value to -1 when the total number of frames
is unknown. After processing coordinates, the actual number of frames read
was not being passed to actions (so this bug may have been affecting more
than just the average command). Anyway, I've attached a patch that updates
each action with the total number of frames read. Patch works on both
current RC and AmberTools-1.3 versions of ptraj.c, so it can be used as a
bugfix. Patch as is needs to be applied in the /src/ptraj/ directory.

-Dan

On Fri, Apr 16, 2010 at 4:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> I can confirm this bug. Appears to be a problem with compressed
> trajectories - if I decompress the trajectory first it works fine. Looking
> into the bug now...
> -Dan
>
>
> On Fri, Apr 16, 2010 at 3:53 PM, Tom Joseph <ttjoseph.gmail.com> wrote:
>
>> Apologies in advance for the probable silliness of this question, but
>> with the 14 Apr release candidate of AmberTools (compiled with
>> "-nobintraj -noX11 -nosleap gnu"), the following ptraj commands do not
>> generate an average structure in foo.pdb, whereas they do with the
>> AMBER 10-era ptraj:
>>
>> trajin md5.trj.gz
>> average foo.pdb
>> go
>>
>> ...where md5.trj.gz is a gzipped mdcrd trajectory. It isn't clear to
>> me from the documentation in CVS (or else I missed it) how my commands
>> are incorrect. I have the same (lack of) result with CVS AMBER 11's
>> AmberTools. The ptraj output is below.
>>
>> Thanks,
>> --Tom
>>
>> $ $AMBERHOME/bin/ptraj solute.pdb
>>
>> \-/
>> -/- PTRAJ: a utility for processing trajectory files
>> /-\
>> \-/ Version: "AMBER 11.0 integrated" (4/2010)
>> -/- Executable is: "/home/josept02/build/14apr10/amber11/bin/ptraj"
>> /-\ Running on 1 processor(s)
>> \-/ Reading PDB file "solute.pdb": 12004 atoms found!!!
>> Found 720 residues
>>
>> PTRAJ: Processing input from "STDIN" ...
>> trajin md5.trj.gz
>>
>> PTRAJ: trajin md5.trj.gz
>> Checking coordinates: md5.trj.gz
>> checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory file: md5.trj.gz
>> If this is not a compressed file then there is a problem
>> Rank: 0 Atoms: 12004 FrameSize: 291723 TitleSize: 81 NumBox: 3 Seekable 0
>>
>> average foo.pdb pdb
>>
>> PTRAJ: average foo.pdb pdb
>> Mask [*] represents 12004 atoms
>> go
>> [No output trajectory specified (trajout)]
>>
>> PTRAJ: Successfully read the input file.
>> Coordinate processing will occur until EOF (unknown number of
>> frames).
>> Summary of I/O and actions follows:
>>
>> INPUT COORDINATE FILES
>> File (md5.trj.gz) is an AMBER trajectory (with box info)
>> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>>
>> ACTIONS
>> 1> AVERAGE: dumping the average of the coordinates to file foo.pdb
>> start: 1 Stop [at final frame] Offset: 1
>> Atom selection * (All atoms are selected)
>> Output file information: File (foo.pdb) is a PDB file
>>
>>
>> Processing AMBER trajectory file md5.trj.gz
>>
>>
>> Set 1 .................................................
>> - snip -
>> Set 3950 .................................................
>> Set 4000 100%
>>
>>
>> PTRAJ: Successfully read in 4000 sets and processed 4000 sets.
>>
>> Dumping accumulated results (if any)
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
>
>
>


-- 
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854



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Received on Fri Apr 16 2010 - 15:00:02 PDT
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