Dear friends.
I am new to amber MD and I am working on a terinery complex
simulation. There is a ZN2+ ion at the active site coordinately bonded to
HISD, ASP and CYS and also with a drug molecule of interest. I need to
restrain the bonds and maintain the charge on the ion. This was quite easy
in gromacs, where in we can specify them in specbond.dat and parameters for
Zn are automatically calculated. but this is not the case using with tleap
and antechamber ( found a tutorial of rosswalker
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section1.htm
but
this is quite outdated and doesnt work well with amber11's tleap). I Need to
perform simulations on a set of docked complexes. I have a fermi card and
md-run in gromacs is not quite evolved as pmemd.cuda. Any help is highly
appreciated.
thanks and regards
bharath
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Received on Sun Mar 06 2011 - 12:30:04 PST
