Hi,
you could use the AddToBox utility.
(follow the tutorial
http://ambermd.org/tutorials/advanced/tutorial13/Solvation.html)
After creating 3 pdb files (containing a single methanol, a single
chloroform and a single water molecule), you can simply fill your box with
the right amount of molecules necessary to reach the desired stoichiometry.
Of course, nothing will be equilibrated, so you'll need to equilibrate and
add again new molecules probably...
Hope it helps
Bye
giovanni
Dr. Giovanni Maria Pavan
SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
Centro Galleria 2, Manno 6928, Switzerland.
e-mail: giovanni.pavan.supsi.ch
skype: giovanni_pavan
phone: +41 58 666 65 60
-----Messaggio originale-----
Da: rameshwar prajapati [mailto:rameshwar.niper.gmail.com]
Inviato: domenica, 27. novembre 2011 18:35
A: AMBER Mailing List
Oggetto: [AMBER] how to prepare 4:4:1 methanol-chloroform-water mixture
Hi,
I need your help.
How could I prepare a 4:4:1 methanol-chloroform-water mixture water box
around a protein.
I would be greatly thankful if anybody could help me out.
--
With regards,
RAMESHWAR PRAJAPATI
DEPT. OF PHARMACOINFORMATICS
NIPER S.A.S NAGAR (MOHALI)
09569089451
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Received on Mon Nov 28 2011 - 01:30:04 PST
