Kamali,
Indeed, you will need to use PBSA or any other PB programs for EACH
snapshot to obtain its potential map. There is no way out. I see no
problem of using Amber/AmberTools if you have a linux on your PC or if
you have a Mac. So far we don't support Windows.
We usually don't use PB for a full box of explicit water molecules. It
beat the purpose of using PB or GB, which is implicit water. Of
course, if you have enough memory on your computer, the PBSA program
certainly can handle the fully solvated simulation box.
Ray
On Sat, Jan 26, 2013 at 7:00 AM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Dear Amber users,
>
> I have a question about generating electrostatic potential maps for
> snapshots of a trajectory. I've read that it's possible to us PBSA within
> AMBER, but this sounds like one would have to use an mdin file to computer
> different snapshots. This sounds like a time-intensive method that also
> needs to use AMBER itself; I'm wondering if there is a way I can use
> AmberTools or any other program on my personal computer. I'm also not sure
> if it's appropriate to use PBSA with the explicit-solvent simulations that
> I want to analyze.
>
> I've been looking into the APBS software (
> http://www.poissonboltzmann.org/apbs) for which VMD has a plugin, but that
> requires loading of a parm file, and since I use parmbsc0+chiOL3 as well as
> a different parm file for a noncanonical base pair, I'm not sure of a
> simple way to load the force field that I'm using.
>
> I realize this is a broad question, so any insight that anyone can provide
> would be greatly appreciated!
>
> Thank you all,
>
> Kamali Sripathi
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Received on Sat Jan 26 2013 - 08:30:02 PST
