AMBER Archive (2003)

Subject: Re: ptraj residue number out of range

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Feb 25 2003 - 11:31:14 CST

Dear Guilio,

your are right - I didn't pay attention. ptraj uses a pdb library with
the source in $AMBERHOME/src/ptraj/pdb. Formats for reading and writing
are in read_format.i and write_format.i, resp. For writing ATOM lines
with atom numbers > 99999 and residue numbers > 9999, I would exchange
the line

"ATOM %5d %-4s%c%-4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %3D"

in write_format.i with

"ATOM %6d%-4s%c%-4s%c%5d%c %8.3f%8.3f%8.3f%6.2f%6.2f %3D"

.

This is analogous to what has been done for leap. A similar change needs
to made in read_format.i .

Perhaps Th. Cheatham might comment if this should be included in ptraj
in a more general way?

Best regards

Holger

> Dear Holger,
> as far as I understand, bugfix.8 is for leap and not ptraj. How to make
> a similar correction in ptraj? Thanks again.
> Giulio
>
> Holger Gohlke wrote:
> >
> > > I noticed that the residue number of a pdb file generated by ptraj
> > > goes out of range when exceeding 4 digits (9999). Any help on
> > > where to modify the format line in the code? Thanks,
> > > Giulio
> >
> > Have a look at bugfix.8 for amber7
> > (http://www.amber.ucsf.edu/amber/bugfixes/7.0/bugfix.8).
> >
> > Best regards
> >
> > Holger
> >
> > > --
> > >
> > > Giulio Rastelli
> > > Dipartimento di Scienze Farmaceutiche
> > > Universita di Modena e Reggio Emilia
> > > Via Campi 183
> > > 41100 Modena - ITALY
> > > -------------------------------------
> > > tel 0039-059-2055145
> > > fax 0039-059-2055131
> > > ------------------------------------- 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++