Dear Amber community,
I have run a 110 ns MD for an RNA system explicitely solvated by TIP3 water molecules. I would like to run another 50 ns MD for the system before I start analyzing the trajectory. However, there appears to be a problem with the last mdcrd file (acquired at the end of 110 ns MD). After going through each line in the mdcrd file i figured that the format of the mdcrd file was disrupted by huge numbers as examplified below (talking about the first line compared to the conventional second line):
Line 1) -1079.9300543 -31.8968786 259.2745548-1079.0899662 -31.8930939 258.0129848
Line 2) -286.6010762 12.6202845 20.8281542-286.9375394 13.5078975 20.704998
Is there any way to correct (??reformat??) line 1 (especially the first number in Line 1) so that I can continue my MD experiment?
best regards,
jenk.
Cenk Andac, M.S., Ph.D. Student
School of Pharmacy at
Gazi University-Ankara Turkiye
Address: Bandirma Sok. No:6
Etiler, Ankara, 06330 Turkey
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
---------------------------------
Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 25 2007 - 06:07:07 PDT
