Re: AMBER: question about formatted mdrcrd files...

From: David A. Case <>
Date: Sun, 22 Jul 2007 16:30:06 -0700

On Sun, Jul 22, 2007, Cenk Andac wrote:
> 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?

If there are only a handful of such entries, you could reformat by hand, to
remove the 13-digit entries (so all entries are 12 digits). Otherwise, you
need to go back to the last restart before this one, and start there, setting

[It would be on interest to know what compiler you used: all compilers I am
aware of would print "***" in a field if 13 characters were needed by only
12 were called for in the format statement (which in this case is 6f12.7).
But your system seems more like "C", in that it added an extra digit and
pushed everything else to the right. And, is this sander or pmemd? Which


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Received on Wed Jul 25 2007 - 06:07:09 PDT
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