On Fri, Feb 02, 2018, Andrew Schaub wrote:
>
> 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*.
Taisung's advice is correct. Just to add a little: it is the box lengths and
angles in the restart file that are used, not the ones in the prmtop file.
This is because the prmtop stays constant (say in NPT runs), whereas the
parameters in the restart file may be changing. (In this particular case,
the octahedral angle is actually constant, but the code doesn't know that.)
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 04 2018 - 06:00:04 PST
