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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 29 2014 - 13:00:02 PDT
