From: Josef Scheiber (Josef.Scheiber_at_mail.uni-wuerzburg.de)
Date: Mon Dec 08 2003 - 02:50:37 CST
Hi all,
the official guide for the PDB format can be found at
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
But be careful: A lot of files in the database don't match this standard, if
you're interested, there is a paper about this:
The Protein Data Bank: unifying the archive
Describes the ongoing efforts that are underway to address the inconsistency in
the archive. (2002) Nucleic Acids Research, 30 (1), pp. 245-248.
It's also possible that your topology file doesn't contain an entry for your
residue "PEU", maybe you should also check this.
Josef Scheiber
Zitat von yxiong_at_mail.ccnu.edu.cn:
> Hi,
> Please note that PDB files are column based, and everything must appear in
> the
> correct column(s). In other words, it's not safe to add or remove spaces
> between
> data in a PDB file. You can compare your file to a standard PDB file (e.g.,
> one
> downloaded from the Protein Data Bank), and make sure that every field
> (especially
> the resid field) be in the same columns in both files.
>
> Ying Xiong
>
> >From: AHMET BAKAN <ABAKAN_at_KU.EDU.TR>
> >Reply-To:
> >To: namd-l_at_ks.uiuc.edu
> >Subject: namd-l: PSF generation
> >
> >Hi all,
> >I have defined a residue of 127 atoms for a polymeric chain sample. PDB file
> for
> one residue ends as below:
> >ATOM 121 H37A PEU 1 10.644 13.121 4.7ATOM 122 H37B PEU
> 1
> 10.636 11.621 3.7ATOM 123 H35A PEU 1 8.672 12.464
> 5.9ATOM
> 124 H35B PEU 1 8.331 12.205 4.2ATOM 125 HN7 PEU 1
> 10.782
> 12.241 7.5ATOM 126 HN8A PEU 1 14.809 13.096 7.1ATOM 127
> HN8B
> PEU 1 14.063 12.139 5.8The problem is that NAMD psfgen finds no
> residue. When I shift residue_name column to one left, psfgen finds a residue
> but
> does not read last 40 atoms. Is column with restricted in PDB files?? How can
> I
> overcome this problemThank you very much,Ahme
> > ==============ABC==============
> >Ahmet BAKAN
> >Chemistry, JunioKoc Universiabakan_at_ku.edu.trICQ
> #8616769http://home.ku.edu.tr/~abaka
> >
>
>
Josef Scheiber <Josef.Scheiber_at_mail.uni-wuerzburg.de>
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