On Mon, Jun 11, 2012 at 6:45 PM, Do-Yong Kim <dxk102.case.edu> wrote:
> Dear Amber Users,
>
> I am trying to combine 908 pdb files into one mdcrd file. So far I was't
> successful with this process. I am not processing all of the sets into
> mdcrd file.
>
> I get final result like this
>
> PTRAJ: Successfully read in 908 sets and processed 1 sets.
> Dumping accumulated results (if any)
>
> last few input file lines to ptraj is
>
> trajin bc9.pdb.33.new 907 1 907
> trajin bc9.pdb.58.new 908 1 908
>
Do not put the numbers at the end of the trajin statements. If I
understand correctly, each PDB has only 1 frame, and you have 908 such PDB
files. For instance, the line:
trajin bc9.pdb.33.new 907 1 907
loads the bc9.pdb.33.new file, beginning with the 907th snapshot (which
doesn't exist, because each PDB has only 1 snapshot) and ending with the
1st (which doesn't make sense, but perhaps this is not explicitly checked
for in ptraj?), taking every 907th snapshot. This will not extract any
snapshots. In fact, the only line that will extract a snapshot is the
first line (hence the message you are seeing).
Long story short, remove the 3 numbers at the end of each trajin statement
and try again.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 12 2012 - 19:30:02 PDT
