Dear Amber users,
I tried to neutralized the protein using counter ions in Leap AMBER 7, here is my
leap script,
source leaprc.ff99
set default PBradii bondi
loadOff Ca.Off
hcam = loadPdb hcam.H.pdb
addIons hcam Na+ 0
saveAmberParm hcam hcam.top hcam.crd
quit
from this step, I have no problem,the topology and coordinate file recorded
properly. However when I did minimization using sander, the atom type IP which
is correspond to the counter ion Na+ was not recognized. Here is my input file
the minimization:
&cntrl
imin = 1, maxcyc = 500,
ntb = 0, igb = 2, cut = 300.0,
igb = 2, saltcon = 0.2, gbsa = 1,
ntpr = 10, ntx = 1,
&end
restrained atoms
5.0
RES 1 148
END
END
What is wrong with above input file? How to make sander recognize those counter
ions? Any valuable input is welcome.
Thank in advance.
Rukman
Laboratory of Biodynamics
Tokyo Insitute of Technology
--
rhertadi_at_bio.titech.ac.jp
Received on Thu Mar 28 2002 - 13:55:33 PST
