[AMBER] Update 12 for AmberTools 13: CPPTRAJ

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 8 Jul 2013 16:32:28 -0600

Hi All,

I would like to announce update 12 for AmberTools 13, which contains
more enhancements to and bug fixes for CPPTRAJ. This updates CPPTRAJ
to version 13.12 and includes the following:

1) CPPTRAJ will no longer automatically fail when reading/generating
topology files with molecules containing non-sequential atoms; instead
it will proceed without molecule/solvent information; only actions
that depend on such information will not work.

2) Fix error compiling with old GNU compilers: "DihedralSearch.cpp:53:
error: unknown escape sequence '\*'"

3) When processing command line flags do not process input files until
after all other flags processed.

4) Add 'center2' and 'nointramol' keywords to 'radial' action. The
'center2' option is for using the center of atoms in mask 2 (similar
to center1). The 'nointramol' option ignores intramolecular distances.
The 'center1', 'center2', and 'nointramol' keywords are mutually

5) PDBs generated by the 'mask' action no longer contain molecule
information (i.e. TER cards). Such information may be added if desired
(and if the PDB is valid) by re-reading the PDB back into CPPTRAJ.

6) Fix the 'parmbox' command so that explicitly specifying the parm
index immediately after the command is no longer required (it can be
placed anywhere or omitted to use the default topology).

7) Fix potential error in autoimage when using multiple topologies in
a single run.

8) Fix writing of PDB files when molecule information not present in Topology.

9) Fix up residue numbers in NAstruct data set legend strings.

This update is currently available. To apply, simply re-run configure
from $AMBERHOME and re-compile.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 08 2013 - 16:00:02 PDT
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