[Ian Slaymaker asked about the nucleosome example in the nab manual, reporting
a "Atom O3' not in residue A" error message.]
I'm not sure I understand exactly how you got to this result. Here's what
I have tried:
a. Go to $AMBERHOME/AmberTools/examples/nab. There program_10.nab and
getbase.nab are what you need. I think these files are correct, even though
the version in the manual is out of date (as you have noted.) Compile like
this:
nab program_10.nab getbase.nab
b. Then running:
a.out 10 94 20.0 <=== just wild guesses for the arguments!
yields a "nuc.pdb" file.
Can you see if this works for you (with AmberTools 1.5 if possible). There is
a small chance that I am relying on some fix that happened since AmberTools
1.5 was released, but I hope not. I think more likely that there is still
some difference between the files in the example directory (which we actually
check) and the code in the manual (which might have typos or other errors).
...hope this helps...dac
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Received on Wed Feb 15 2012 - 14:00:01 PST
