On Wed, Oct 14, 2015 at 5:12 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> The first error you reported had to do with using a version of MMPBSA.py
> that was released over 5 years ago, that you somehow unpacked on top of
> AmberTools 15. This is not at all the recommended or documented way to
> install AmberTools, and it is a way that does not work.
>
> no i installed new verssion of AmberTools 15 but it also didn't work .
> kindly help me by giving an example how can i properly install and can run
> MMPBSA.py
Your response makes it seem like you only read and listened to a small
part (and perhaps the least relevant part) of my original answer. You are
making it exceedingly difficult to provide help, as it is unclear at every
turn whether you have tried (or even read) what was suggested before, how
much of it you understood, and how comfortable you are with the basic
concepts of operating in a Linux/Unix environment. The help that I can
reasonably provide necessarily assumes some level of familiarity and
competency with the Unix command-line.
This requires some effort on your part to achieve the required level of
familiarity so that we can effectively communicate (indeed, *everybody*
starts from the beginning at some point). Until that happens, continuing
this thread will be an effort of frustration -- you derive no benefit from
my help and I feel like I am being ignored and my time wasted.
> i have very little time and i am worried about my project i am unable to
> understand your instructions easily
Unfortunately, based on the conversation here, learning enough to
successfully carry out these studies is going to take time. If it is time
you don't have, then I would suggest searching for a knowledgeable
collaborator that can help. It's unreasonable to expect that skills people
spend an entire Ph.D. developing can be, even in small part, picked up in
spare time over a weekend (or something similar).
that you discuss prior so please guide me about these commands by giving me
> simple demo
The simple demo is the tutorial. There is no way I can do a better job of
providing a demo over a mailing list than the tutorial does.
as its hard for me to get about these commands and i only want to use
> MMPBSA.py package from AmberTools 15 or 14 .
I think this belies an understanding of what MM/PBSA analyses are. This
is a post-processing technique that you use on a simulation *you have
already run*. You can't "just run MMPBSA.py". You need to run a basic MD
first, most likely parametrizing a small organic molecule that will play
the role of "ligand" in this analysis. So the tutorials B0 (
http://ambermd.org/tutorials/basic/tutorial0/) and B4 (
http://ambermd.org/tutorials/basic/tutorial4b/) are not only better places
to start for you, they are actually the first steps in an MM-PBSA study,
anyway. So please work through these tutorials -- they were written
precisely to help people like you ease into using Amber.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 14 2015 - 06:00:04 PDT
