Hello All,
I would like to announce update 10 for AmberTools 13, which contains
several enhancements to and bug fixes for CPPTRAJ. This updates
CPPTRAJ to version 13.10 and includes the following:
1) Adds the 'mindist' action. This will calculate the minimum distance
between atoms in two non-overlapping masks. Usage:
mindist [<name>] <mask1> <mask2> [out <filename>] [noimage]
Imaging is performed by default when box information is present unless
the 'noimage' keyword is given.
2) Fix normalization of RDF integral for 'radial intrdf'. Results now
match PTRAJ.
3) cluster: Add timing data to clustering and fix potential bugs in
average cluster distance output when number of cluster frames is
large. Also add option 'sievetoframe' to DBSCAN. When performing
DBSCAN clustering with a sieve, sieved frames are added to existing
clusters based on distance to the closest cluster centroid. While this
is fast, it does not distinguish sieved frames as noise. The
'sievetoframe' option adds sieved frames to the cluster with the
closest centroid only if the sieved frame is within epsilon of a frame
in that cluster. This option is much slower but will identify sieved
frames that should be noise.
4) Fix 'multidihedral' so that all nucleic acid chi angles ('chin')
are correctly recognized. Previously, pyrimidine nucleic acid chi was
not properly recognized.
5) 'jcoupling' no longer fails when an atom is not found for a
residue/dihedral combination, it continues to the next dihedral.
6) Add 'printatomnum' option to hbond for printing atom numbers in
hbond average output. Standard output:
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
ILE_19.O THR_12.H THR_12.N 69 0.6900
2.8626 160.5248
With 'printatomnum':
ILE_19.O_293 THR_12.H_166 THR_12.N_165 69
0.6900 2.8626 160.5248
7) Fix potential segfault in 'crdfluct' analysis when COORDS are empty.
8) Prevent tests that depend on NetCDF from running when compiled with
'-nobintraj'.
9) Fix various typos.
This update will be available soon (within the next day or so). To
apply, simply re-run configure from $AMBERHOME and re-compile.
Also, for those interested, the following recent publication goes into
the workings of PTRAJ and CPPTRAJ in a little more depth:
http://pubs.acs.org/doi/abs/10.1021/ct400341p
-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 Wed Jun 19 2013 - 10:30:03 PDT
