Hi,
Instead of editing your topology and restart files directly, you can
also use the cpptraj commands 'parmbox' and 'box' to edit them
respectively. In particular there is a flag (IFBOX here:
http://ambermd.org/formats.html#topology) that must be set to 2 in the
topology file for truncated octahedral boxes.
-Dan
On Fri, Feb 2, 2018 at 1:07 PM, Andrew Schaub <aschaub.uci.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Feb 09 2018 - 04:30:01 PST
