AMBER Archive (2002)

Subject: Water molecule numbering

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Thu Jul 25 2002 - 17:28:25 CDT

Hi All,

  I have a question about residue numbering of water molecules. When I load a PDB file which contains bound waters onto Leap, assign parameters, save it with "saveamberparm", and then generate PDB file from CRD and TOP file with "ambpdb" command, residue numbering of water molecules are automatically changed.

  Have anybody found the problem before? Only me? If this is the case, is there any rule in the renumbering?

Masaki Tomimoto