Hi Andrew,
Try to modify the box info in your inpcrd file (at the very end). If it is
not in text format, use cpptraj to convert it to plain text first.
Taisung
-----Original Message-----
From: Andrew Schaub [mailto:aschaub.uci.edu]
Sent: Friday, February 2, 2018 1:08 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] setbox for octahedral
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 02 2018 - 14:30:01 PST
