Dear All.
I try to do a simple MMPBSA calculation on a zinc-enzyme with MMPBSA,py.
Since what I concern is the relative binding energy, not absolute binding
energy.
I assume that the error is systematic, and could be canceled out.
This is the my force field file:
metal.mpg
MASS
Zn 65.38 0.00
NONB
Zn 1..850 0.06
metal.prp
0 0 1
ZN2
ZN2 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 Zn Zn M 29.683 127.561 -18.450 2.00
DONE
STOP
Those parameter was found from the website:
http://archive.ambermd.org/201001/0254.html
However, I got this from the output file: "bad atom type: Zn".
Did i give the wrong parameters for Zinc?
Besides, the MMPBSA calculation ended with the error "PB bomb in
pb_reslist(): maxnbr too small".
It is said that the issue could be solved by modifying the cutres.
However, the option "cutres" is not found in AMBER11 any more.
Is there a similar option for this issue in AMBER11?
Any help could be appreciated!
Best,
Zhihong
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Received on Thu Dec 02 2010 - 10:00:02 PST
