AMBER Archive (2004)

Subject: Re: AMBER: why delete water molecule

From: Oliver Hucke (
Date: Tue May 04 2004 - 11:23:01 CDT

In this context it might be interesting to look at the HB2NET command of
the program WhatIf of Gert Vriend ( This
command optimizes the overall hydrogen bond network within a protein.
If the program is not installed on an available machine, the www
interface is an alternative:

What I am not sure about is the compatibility of the WhatIf output with
what AMBER expects as input. Some conversion might be necessary...

Best regards,

Dr. Yong Duan wrote:
> Dear Helios:
> Although it has been advised that the crystal waters should be removed,
> one certainly has the option not to do so. It is probably a good idea to
> retain the crystal waters. However, a technical challenge for not
> removing the crystal water is the assignment of hydrogens. You probably
> can try to assign these hydrogens at randomized orientation and optimize
> them by MD. But you have to write your own code to do it.
> yong
> On Tue, 4 May 2004, Helios Chen wrote:
>>Dear all, I saw some papers about run molecular dynamic with adding solvent(ex. TIP3P, TIP4P), but I have a question. Why they delete all water molecules in origin PDB file before adding solvent? Are there any difference between them? In another word, does the energy for adding solvent with deleting all water molecules differ from adding solvent without deleting any water molecules?
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Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: _______________________________________________________________

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