Re: psfgen: more problem

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Sep 08 2008 - 14:17:28 CDT

On Tue, 9 Sep 2008, Rudra Banerjee wrote:

RB> As i wrote in earlier mail, the problem is also happenning for DNA
RB> molecules as well> the 1LAE structure is also giving the error like
RB>

[...]

RB>

RB> part of pdb(pdb code:1LAE) file is added as it is too big to copy
RB> here. the problem is its not "understanding". A,T,G,C . why it is
RB> so?

most likely, because your file is not conforming to the PDB standard.
please see below how the columns are shifted, thus in the second
part it'll read 'C A' as residue name and not 'C' or 'A'.
there'll be funny things happening to your coordinates as well.

please read the documentation about the .pdb file format standard
very carefully and correct your pdb file.

cheers,
   axel.

RB> CRYST1 1.000 1..000 1.000 90.00 90.00 90.00 P 1 1
RB> ATOM 1 O5' C A X 1 1.477 -17.625 15.716 1.00 0.69 O
RB> ATOM 2 C5' C A X 1 2.783 -18.207 15.687 1.00 0.69 C
RB> ATOM 3 C4' C A X 1 3.875 -17.138 15.666 1.00 0.59 C
RB> ATOM 4 O4' C A X 1 3.727 -16.259 14.515 1.00 0.53 O
RB> ATOM 5 C3' C A X 1 3.793 -16.250 16.893 1.00 0.55 C
RB> ATOM 6 O3' C A X 1 5.095 -15.838 17.309 1.00 0.50 O
RB> ATOM 7 C2' C A X 1 2.990 -15.075 16..428 1.00 0.50 C
RB> ATOM 8 C1' C A X 1 3.387 -14.921 14.972 1.00 0.46 C
RB> ATOM 9 N1 C A X 1 2.287 -14.338 14.161 1.00 0.45 N
RB> ATOM 10 C2 C A X 1 2.599 -13.276 13.317 1.00 0.38 C

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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