AMBER: question about formatted mdrcrd files...

From: Cenk Andac <>
Date: Sun, 22 Jul 2007 09:47:45 -0700 (PDT)

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,



   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

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Received on Wed Jul 25 2007 - 06:07:07 PDT
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