AMBER Archive (2004)

Subject: AMBER: Parameters for ions?

From: nie beining (nie_b_at_yahoo.com)
Date: Fri Apr 02 2004 - 12:15:51 CST

Dear Amber users,
 
      We would like to see simulation of Ammonium Sulfate in bulk water with Amber. But I don't know how the parameters, i.e., prep and frcmod files for ammonium sulfate are constructed. Are there any users who have experience in this kind of simulation before? I searched the webpages containing following parameters for Ca2+ ions:
 
prep file:
CAL
CAL INT 0
CHANGE OMIT DU BEG
 0.0
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
   2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
   3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
   4 KA KA M 29.683 127.561 -18.450 2.00

frcmod file:

Ca2+ vdw parameters from Concanavalin A study

MASS

KA 40.00 0.00

NONB

KA 1.7900 0.0140

Can someboby please explain these parameters for me? Thanks in advance!

regards,

Beining

---------------------------------
Do you Yahoo!?
Yahoo! Small Business $15K Web Design Giveaway - Enter today
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu