Re: AMBER: Hydration points

From: Cenk Andac <>
Date: Wed, 30 May 2007 14:23:33 -0700 (PDT)

Dear Prof. Simmerling,

Thank you for your suggestion. I can now determine hydrations points in binding sites.

best regards,


Carlos Simmerling <> wrote: you can use the ptraj grid command.
page 252 of the amber9 manual.
also web search for ptraj water grid.

On 5/29/07, Cenk Andac <> wrote:Dear Amber community,

I was wondering if it is possible to determine hydration points in a TIP3 water solvated binding site over an MD trajectory? If so how?

best regards,



Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336 
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail:
Stony Brook, NY 11794-5115          Web:
   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey 
 Cell: +90-(536)-4813012
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Received on Sun Jun 03 2007 - 06:07:15 PDT
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