AMBER Archive (2003)

Subject: solvatecap

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Wed Jan 15 2003 - 08:48:05 CST

Hi,
I am trying to run a belly dynamics. I have defined a solvatecap and working
with a number of residues close to 10000
But in the MD run, the outpus says that the moving residues should be at the
start of the molecule.
That seems that I should redefine the crd and top files with the moving residues
at the beginning of the pdb? The problem is that the water molecules are always
placed at the end with the solvatecap option.
Has anyone gon through the same problem?
Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802