Good Morning,
I am trying to run T.I. on my system. I first ran a 100 ns NPT simulation
to equilibriate my system prior to beginning T.I. I extracted my water+ions
and receptor as two separate PDBs. I then run LEAP again, I specify my box
lengths from the restart file from my equil. and generate new prmtop and
inpcrd files. These have two receptors, so I use parmed to create merged
prmtop and inpcrd files. Everything looks fine. As there is no solvateoct
command in leap, I manually edit the prmtop files like so:
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
*1.09471219E+02* 7.70090000E+01 7.70090000E+01 7.70090000E+01
So I replace the 90 degree angle with *1.09471219E+02*. When I begin my
simulations they start off as octahedral and then morph into boxes. Pmemd
doesnt seem to be reading my manually entered box dimensions. Is there a
workaround, or should I just do a regular box?
Best Regards,
Andrew Schaub
PhD Candidate, Chemistry
Tsai Lab, University of California, Irvine
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Received on Fri Feb 02 2018 - 10:30:02 PST
