Hi All,
I am simulating my protein which consists Calcium ion in its active site
along with bound ATP. I downloaded the parameters from Manchester site and
prepared my system well. I changed the atom type to C0, the atom type
specified in AMBER for calcium. Now I ran my simulation for 20 ns. I found
during simulation, ATP came out of the cavity.
Lately, I figured out that for calcium there is no charge when I generated
pdb file from .rst file.
This is how calcium ion looks like in my pdb file:
ATOM 5699 C0 CAL 366 41.302 40.540 39.770 1.00 0.00
C
and below mentioned is the frcmod file:
Ca2+ and Mn2+ vdw parameters from Concanavalin A study
MASS
MN 55.00 0.00
C0 40.00 0.00
NONB
MN 1.6900 0.0140
C0 1.7900 0.0140
And below mentioned is the prepin file:
0 0 2
------calcium--------------
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 C0 C0 M 14.110 23.997 25.894 2.00
DONE
------manganese--------------
MNG
MNG 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 MN MN M 29.683 127.561 -18.450 2.00
DONE
STOP
Kindly let me know where I am doing mistake..
Thanks and Regards,
Hirdesh
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Received on Tue Dec 25 2012 - 12:30:03 PST
