Hi Jason,
Thank you very much for your advice. I am repeating my simulations, since I
think the system did not minimize correctly, and I will get back to you
later since this may be a factor.
Holly
On Thu, May 29, 2014 at 1:40 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, 2014-05-29 at 13:28 -0600, Hallel Freedman wrote:
> > Hi Jason,
> > Option 1 doesn't seem to work because, this way, I calculate positive
> large
> > values of deltaG.
>
> That's weird. You are sure it is the nonpolar solvation term causing
> that? What is your surface tension? The nonpolar term with inp=1 is
> typically fairly small, so I doubt using inp=2 is a fix for your
> problem. (inp=1 is a much simpler model)
>
> > I haven't tried option 2 yet.
> > As far as option 3, I would like to try it, but because I am running on
> > many ligands, I need to use parmed.py instead of xparmed.py. Would you
> mind
> > giving me an example please of what I would write in parmed for this?
>
> Something like:
>
> change ATOM_TYPE <mask> <new value>
>
> For each atom type you need to change, you'll need a different "change"
> command.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu May 29 2014 - 15:30:02 PDT
