On Thu, Mar 10, 2016 at 5:14 AM, David A Case <david.case.rutgers.edu> wrote:
> On Wed, Mar 09, 2016, Dan Roe wrote:
>>
>> Try using cpptraj to convert the restart ....
>
> Note that Bin is already using the cpptraj code:
I realize this - after all, I wrote the code :-)
I recommended using cpptraj instead of ambpdb as a way to debug what
is going on. By design, ambpdb with the cpptraj backend suppresses all
non-error messages (i.e. warnings, general information, etc). When
using cpptraj you can see if say hold1.rst is in another format
recognizable by cpptraj; if the format cannot be detected then maybe
the file itself is just corrupted.
-Dan
>
>> > [01292016]$ /opt/amber14/bin/ambpdb -p m1_watoct.prmtop < hold1.rst >
>> > hold1.pdb
>> > | ambpdb (C++) Version V15.00
>> > | Reading Amber restart from STDIN
>
> My guess(?) is that hold1.rst is a binary restart, and one has to use the -c
> option rather than redirection from stdin:
>
> ambpdb -p m1_watoct.prmtop -c hold1.rst > hold1.pdb
>
> Worth a try, anyway.
>
> ...dac
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 10 2016 - 07:30:03 PST
