On Sat, Nov 07, 2009, liangchen88.ucla.edu wrote:
> I was trying to run the first tutorial (polyA-polyT) provided with
> Amber and got stuck early in the process, because the
> $AMBERHOME/dat/leap/parm/nucgen.dat file in the Amber10 distribution
> is not correct. The file consist of about 380 lines with a single line
> for each atom:
> atom x y z
It actually atom r phi z, in cylindrical coordinates.
> It is different from the format :
> linedifinition atom no. atom name residue name residue no.
> x y z
I'm not sure why you think the latter format is the correct one; nucgen.dat is
not (and is not supposed to be) in pdb format.
> So that i get the empty pdb file after running nucgen .
I guess we would need more details. The origin of your error is not in the
format of the nucgen.dat file.
Alternatives (better!) to nucgen are the fd_helix() routine in NAB, or the
even more powerful Olson group webserver at
http://w3dna.rutgers.edu.
...dac
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Received on Sat Nov 07 2009 - 07:00:04 PST
