Hi Daniel, indeed - in the meanwhile I was using a sed onliner to fix the count of residues in my scripts.
Yes, the substructure section and the rest seems pretty correct. I'm still glad, that I can use the cpptraj mol2 file output.
Because the mol2 output from top2mol2 is even worse and much harder to fix in an automated workflow ;)
Thank you very much for fixing this for the future and many thanks for the support.
All the best
Marko
Hi,
On Mon, Feb 4, 2013 at 12:03 PM, Marko Wehle <Marko.Wehle.mpikg.mpg.de> wrote:
> Because from the cpptraj output, as it has a wrong number/count of resdiues in it's metainfo, e.g. it shows a 1 here, instead of the correct number of residues.
OK, now I see what's wrong. The #substructure count is indeed always
set to '1' in cpptraj-created mol2 files, but the 'SUBSTRUCTURE'
section should still be correct. The workaround for now is to edit the
file and change:
.<TRIPOS>MOLECULE
Cpptraj generated mol2 file.
20922 20850 1 0 0
to:
.<TRIPOS>MOLECULE
Cpptraj generated mol2 file.
20922 20850 N 0 0
where N is the total number of residues in the mol2 file. I will work
on a bugfix in the meantime.
Thanks for the report.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Feb 05 2013 - 13:30:03 PST
