hi all ,
i want to plot a graph for Enthalpy and Entropy with respect to frames or time scale on 1 DCD file is it possible or not ?
and 2ndly how can i calculate Enthalpy energy on every frame forexample if i take 1000 frames then it also calculate 1000 energies of Enthalpy.
hope i clear my point. i also attached a paper in which enthalpy and entropy graph is plotted. i exactly want to plot graph like that.
Best regards,
Ayesha Kanwal
> From: ayesha_comsian.hotmail.com
> To: amber.ambermd.org
> Date: Wed, 14 Oct 2015 23:35:47 +0500
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> Hi jason ,
> i know i really getting too much time from your side but you still guided me in every aspect. As my supervisor said that he will give me prepared DCD files and you only have to put it into the MMPBSA.py to visualize the the results . and then you have to put just MMPBSA.py in your tool on whcih i am working my work is to just embed MMPBSA.py in my tool but how can i do this ? this is the basic senario on my side and could not fixed it at all.
> is there any source of MMPBSA.py that can i use for embedding in my tool as my whole work of programming is in python. Or am i going in a write way?
> that's why i was not focusing on other things and just focusing on MMPBSA.py my supervisor did not help me in any aspect he just say keep searching. there is no one who can help me in this regard i hope that these comments may be helpful for me to tell you what is really going here and you can understand my situation in a better way. you can also give me other suggestion if am going wrong . i am doing my project totally on my own. your suggestion would be very helpful for me
> and i am now learning the basics which you had sent me in the previous mail. your words are very helping for me.
> regards
> Ayesha
>
> > Date: Wed, 14 Oct 2015 08:44:19 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
> >
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 13 2015 - 04:30:05 PST
