Software updates, known 'features', etc.

April 11th, 2006

• molmol v.2K-2 installed clusterwide.

March 20th, 2006

• Haploview and Gold (for population genetics) installed clusterwide.

Nov 29th, 2005

• APBS (for electrostatics calculations) installed on newer nodes.

Sept 19th, 2005

• carma v.0.8 updated clusterwide.

Sept 17th, 2005

• Ribosome v.1.0 installed clusterwide.

Jun 15th, 2005

• PyMol 0.98 installed on newer nodes.
• OpenDX 4.3.2 installed on newer nodes.
• Carma v.0.7 installed clusterwide.

April 22nd, 2005

The CHARMM27 topology file contains an error concerning leucine[1]. The line reading

IC CD1  CD2  *CG  HG    1.5361 110.2600 -116.6300 108.0200  1.1168

should read

IC CD1  CD2  *CG  HG    1.5361 110.2600  116.6300 108.0200  1.1168

The result is that the Cγ's hydrogen ends-up almost exactly between the Cβ and Cγ atoms (instead of its normal tetrahedral position). The tetrahedral coordination of Cγ is then "fixed" during minimisation, but there is a catch : the minimiser may force the tetrahedral coordination by moving the hydrogen atom in the wrong direction. The result will be that for some leucines the Cδ1 and Cδ2 atoms will appear swapped, and thus, the calculated χ2 angles will be wrong (180 degress offset).

The CHARMM27 topology files have been corrected cluster-wide.

April 19th, 2005

Tinker v.4.2 plus FFE (Force Field Explorer) installed on all new machines (server, aspera, pc1, pc2, pc3, pc6, pc8, pc9, pc10).

April 13th, 2005

Gromacs 3.2.1 installed cluster-wide. This is an MPI version prepared with icc.

April 7th, 2005

Curves 5.3 installed cluster-wide.