Re: AMBER: Hydration points

From: Cenk Andac <cenk_andac.yahoo.com>
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,

jenk.

Carlos Simmerling <carlos.simmerling.gmail.com> 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 < cenk_andac.yahoo.com> 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,

jenk
        

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-- 
===================================================================
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: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115          Web:  http://comp.chem.sunysb.edu
=================================================================== 
   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
 
 E-Mail:cenk_andac.yahoo.com
       
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Received on Sun Jun 03 2007 - 06:07:15 PDT
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