AMBER Archive (2009)

Subject: Re: [AMBER] the problem of nucgen.dat

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Nov 07 2009 - 08:51:57 CST

On Sat, Nov 07, 2009, liangchen88_at_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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