Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file

From: Dr. M. Shahid <mohammad.shahid.gmail.com>
Date: Tue, 19 Apr 2016 11:47:02 +0200

Dear Ayesha,

In the advanced tutorial 3, section 2 (
http://ambermd.org/tutorials/advanced/tutorial3/section2.htm) there is a
single prod.in file that is run 4 times to produce prod1.mdcrd to
prod4.mdcrd files. Later in section 3.1 all 4 files are specified to the
mmpbsa script as -y *.mdcrd

hope its clear now?

Best regards,

--
Shahid.
On Tue, Apr 19, 2016 at 11:21 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> Dear Shahid,i didn't get your point from : (thats why there are four or
> more trajectory files
>  resulting from each .mdin file.
>  These files are later combined in for doing further analysis such as
> mmpbsa).kindly explain it to me .
>
>
> > From: mohammad.shahid.gmail.com
> > Date: Tue, 19 Apr 2016 10:12:40 +0200
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file
> >
> > Hi,
> >
> > The trajectory files are split into multiple files due to restarting md
> > from restart files, thats why there are four or more trajectory files
> > resulting from each .mdin file.
> > These files are later combined in for doing further analysis such as
> mmpbsa
> > etc.
> >
> > Best regards,
> >
> > --
> > Shahid.
> >
> >
> >
> > On Tue, Apr 19, 2016 at 9:55 AM, Ayesha Kanwal <
> ayesha_comsian.hotmail.com>
> > wrote:
> >
> > > Hi all,
> > > i have a question about amber advanced tutorial for .mdcrd. there is a
> > > single file of mdcrd named prod.mdcrd and four parameter files. i want
> to
> > > know .mdcrd traj. file is for which parameter file ?
> > > or i have to put four .mdcrd files for all four parameter files?
> > > if in your tutorial there is only one .mdcrd file then what is it's
> > > purpose ?
> > >
> > >
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Received on Tue Apr 19 2016 - 03:00:03 PDT