Hi,
On Wed, Mar 20, 2013 at 11:07 PM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> I have tried your suggestion except upgrading cpptraj (for this I guess I
You should really consider updating and recompiling your AmberTools
installation. There are bugs in your version of the code (not just in
cpptraj) that could affect future results. Re-running configure should
be enough to patch your installation.
> The old box error is gone, but there is still a miss match with number of
> atoms while the number of residues is identical now.
In cases like these it really helps to take a close look at your
structure. The problem is that in the 1PRG structure you have a
C-terminal LEU and an N-terminal GLU, while in the 1FM9 structure you
have non-terminal versions of these residues (hence the extra atoms).
Either remove these residues from both structures, or just remove the
extra terminal atoms in 1PRG.
-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 Thu Mar 21 2013 - 08:00:03 PDT
