AMBER Archive (2007)

Subject: Re: AMBER: Hydration points

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed May 30 2007 - 16:23:33 CDT

Dear Prof. Simmerling,

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

best regards,

jenk.

Carlos Simmerling <carlos.simmerling_at_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_at_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
        

--------------------------------- 

-- 
===================================================================
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_at_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_at_yahoo.com

       
---------------------------------
You snooze, you lose. Get messages ASAP with AutoCheck
 in the all-new Yahoo! Mail Beta. 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu