AMBER Archive (2008)

Subject: AMBER: size of pdb

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Jul 11 2008 - 10:13:57 CDT

Hi Amber Users

I have a pdb fie containing 12180 atoms and 813 residues.
When I load it to leap and add waters/
solvateoct pdb TIP3PBOX 9.
The newly solvated file contains more than 99999 atoms....
and leap replaces the number of atoms beyond 99999 by stars.
I suppose the max number of atoms should not exceed 99999. Also the
number of residues when ever they reach 9999, the count starts from 0.
I am supposed to not exceed 9999 residues as well?
Is there a way to overcome this problem, and reduce the number of
unwanted waters?
Thanks for any help
Regards
Boutheina
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