AMBER Archive (2003)

Subject: Re: Max residues (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Fri Mar 07 2003 - 11:12:54 CST

---------- Forwarded message ----------
Date: Wed, 05 Mar 2003 13:18:36 -0800
From: Holger Gohlke <gohlke_at_scripps.edu>
To: amber_at_heimdal.compchem.ucsf.edu, kinsellg <kinsellg_at_tcd.ie>
Subject: Re: Max residues (fwd)

Hi,

have a look at bugfix.8 for amber7:
http://www.amber.ucsf.edu/amber/bugfixes/7.0/bugfix.8

Best regards

Holger

amber_at_heimdal.compchem.ucsf.edu wrote:
>
> ---------- Forwarded message ----------
> Date: Wed, 5 Mar 2003 08:32:08 +0000
> From: kinsellg <kinsellg_at_tcd.ie>
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: Max residues
>
> Hi all,
>
> Are the maximum number of residues that leap can read in set at 10,000 and
> if so how does one go about increasing this number???
>
> I have created a protein bilayer simulation cell (pdb file), with quite a
> large number of water molecules. The number of residues appears to be too
> much for leap which deletes some of the water molecules present leaving a
> total of 10000 residues in the resulting saved pdb file.
>
> Many thanks,
>
> Gemma
>
> The error:
>
> > a1aa = loadpdb biphasic.pdb
> Loading PDB file: ./biphasic.pdb
> -- residue 10000: duplicate [] atoms (total 39384)
>
> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> (same-name atoms are reduced to a single atom)
>
> Unknown residue: number: 9999 type: Terminal/last
> .relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: sequence: 10000
> Created a new atom named: within residue: .R< 10000>
> total atoms in file: 79952
> The file contained 1 atoms not in residue templates 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++++++++++