Hi,
On Mon, Jun 25, 2012 at 3:41 PM, Mahendra B Thapa <thapamb.mail.uc.edu> wrote:
> Warning: Valence not found for for [Na+ ], using max valence (7)
> Let me help to understand what it stands for. I had used Na-atom to
> neutralise in leap process.
Short answer: This message can be safely ignored.
Long answer: Cpptraj does a very simple check when generating bond
information for structures (such as PDB files) to make sure that e.g.
hydrogen isn't making 3 bonds or something (if it does you get another
warning). In this case cpptraj didn't recognize the sodium ion (the
next release of cpptraj will have a more complete atom roster);
however, the code does recognize ions in general and so it won't
create covalent bonds for them. The check is informative only and does
not affect results.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
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 Mon Jun 25 2012 - 20:00:03 PDT
