AMBER Archive (2004)

Subject: AMBER: protein is out of the water box

From: Feng, Hanqiao (NIH/NCI) (
Date: Tue May 25 2004 - 17:35:01 CDT

Hi all,
  I am a new user of AMBER. I tried to follow one of the AMBER Tutorials "
loop dynamics of the HIV-1 integrase core domain(from Matt Lee)" to prepare
the sample for minimization. The program just works fine. The only thing I
changed is to switch "solvateBox mol WATBOX216 10" to "solvateBox mol
TIP3PBOX 10" because the first didn't work. But finally I used ambpdb to
convert the parm and crd files to pdb file, I found the protein is out of
the water box, they are totally separated. Could you please tell me what's

Lab of Biochemistry
NCI/NIH, Bethesda, MD

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