AMBER Archive (2009)

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

From: liangchen88_at_ucla.edu
Date: Sat Nov 07 2009 - 21:48:54 CST

  linedifinition atom no. atom name residue name residue no.
>> x y z
  That is the format in the manual of Amber10.So,I think the that is
right format.
  We were trying yo run a tutorial.According to its steps,we want to
use nucgen.dat to build a PDB file for a nucleic acid.This is method
is similar to homolog modeling.But the final PDB we got is empty.
  I don'n know why?

Quoting case <case_at_biomaps.rutgers.edu>:

> 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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