AMBER Archive (2003)

Subject: Max residues (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Wed Mar 05 2003 - 12:05:20 CST

---------- 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