Carma v.1.2 released.

From: Nicholas M Glykos (
Date: Thu Nov 15 2012 - 04:22:25 CST

Dear All,

It is time for my yearly unashamed 'carma' plug. Be merciful.


                               carma v.1.2

We have released a stable new version (version 1.2) of 'carma' which is a
stand-alone molecular dynamics analysis tool tuned for the DCD-PSF world.
The program is free, open-source software and is immediately available for
download via The distribution
includes source code, documentation and pre-compiled executable images
suitable for GNU/Linux, MacOSX and windows.

WHAT'S NEW : Calculation of fraction of native contacts (Q, Qs, q),
preparation of superposition PDB files (when calculating average structure)
with RMSFs in the B-factor column. Experimental (for linux machines only) :
If an executable for stride is available, carma can now emit the stride-
derived secondary structure assignments.

Carma can calculate the variance-covariance and cross-correlation
matrices, do a principal component analysis using both Cartesian PCA and
dihedral angle PCA, do a PCA-based cluster analysis, remove overall
rotations/translations, calculate the mass-weighted radius of gyration,
calculate the average CA-CA distance map and the rmsd from it (for the
length of the trajectory), calculate the average structure and atomic rms
fluctuations, calculate distances and torsion angles between arbitrary sets
of atoms, calculate solute's entropy using both Schlitter's and
Andricioaei's formulas, allow a primitive quick view of a trajectory on a
X11-capable terminal, calculate CNS- and XPLOR-compatible density maps
representing the average distribution of selected atomic species (eg. ions
or waters), calculate RMSD matrices, export 3D PCA-based landscapes in CNS
map format (suitable for direct input to VMD), etc.


Please note that all correspondence related to carma (comments, suggestions,
bug reports, flames) should be directed to carma's mailing list at (and not, for
example, to the innocent mailing lists that I've misused for advertising
this new version).

Best regards,

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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