**From:** Nicholas M Glykos (*glykos_at_mbg.duth.gr*)

**Date:** Thu Nov 15 2012 - 04:22:25 CST

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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 http://utopia.duth.gr/~glykos/Carma.html 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

http://groups.google.com/group/carma-molecular-dynamics (and not, for

example, to the innocent mailing lists that I've misused for advertising

this new version).

Best regards,

Nicholas

-- 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, http://utopia.duth.gr/~glykos/

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