From: Athanassios Stavrakoudis (astavrak_at_cc.uoi.gr)
Date: Thu Feb 05 2009 - 18:18:08 CST
Dear NAMD users,
We are working on a computer program
for trajectory analysis of protein molecular dynamics.
The program is written in C++,
we will release the full source code by March/April.
We would like to ask interest users to download
and test the program.
Reports and feedback of its usage will be highly appreciated!
Moreover, we expect some ideas and requests,
so we can expand its capabilities.
The program (compiled with gcc) can be download from here:
http://stavrakoudis.econ.uoi.gr/eucb
Examples and tutorials:
http://195.130.120.154/wiki/index.php/Eucb
Currently, there is only on single distribution
based on ubuntu Linux compilation with gcc.
We can add some other (Linux) binaries upon request.
We would like to kindly ask you not to use the namd list
for questions about eucb.
We will create a eucb mailing list soon.
Until then, send your questions directly to:
astavrak _at cc uoi gr
itsouls _at gmail com
Some of the capabilities of eucb:
1. RMSF Root Mean Square Fluctuation of CA atoms
2. RMSD Root Mean Square Deviation of backbone, heavy, side chain and Cá atoms
3. Distance Distance between two user-supplied atoms
4. Angle Angle between three user-supplied atoms
5. Dihedral Dihedral between four user-supplied atoms
6. Torsions backbone and sidechain torsions
7. Contact Analysis of close contacts
8. Contacts between side chain atoms
9. Salt bridges
10. Complex salt bridges
11. Hydrogen bonds
12. Donor focused hydrogen bonds Hydrogen
13. Acceptor focused hydrogen bonds
14. water bridges
15. beta turn search
16. Stacking interactions of side chain ring groups
17. cation/pi aromatic Hydrogen bonds
18. backbone HN/pi aromatic Hydrogen bonds
19. aliphatic H/pi aromatic Hydrogen bonds
20. NOE Calculation
21. 3J coupling constants Calculation of 3J (HN-HA) coupling constants
22. Distance between centers of two user-supplied atom groups
23. pdo Calculation of dihedral angle of orientation
The list is growing...
Best regards,
Thanassis
Athanassios Stavrakoudis
University of Ioannina web: http://stavrakoudis.econ.uoi.gr/
Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
GR-45110, Ioannina tel: +30 651 095 935
GREECE fax: +30 651 095 039
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