hi ,
i need to know why we take 4 parameter files ? solvated complex , complex, receptor and ligand what is the purpose of taking these four parameter files
?
> From: ayesha_comsian.hotmail.com
> To: amber.ambermd.org
> Date: Tue, 19 Apr 2016 15:16:13 +0500
> Subject: Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file
>
> thank you :) first that * command was not working on my system so that's why i could not understand what to do with it now in case if that command didn't work. but now that issue is resolved thank you.
>
> > From: mohammad.shahid.gmail.com
> > Date: Tue, 19 Apr 2016 12:04:39 +0200
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file
> >
> > The script will find out all the files by using the wildcard *.
> > No need to specifiy every file.
> >
> >
> > Best regards,
> >
> > --
> > Shahid.
> >
> >
> > On Tue, Apr 19, 2016 at 12:01 PM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
> > wrote:
> >
> > > Dear Shahid,
> > > I just need to ask that in the script mentioned in tutorial -y *.mdcrd,
> > > Should I specify single mdcrd at a time or should I specify all four mdcrd
> > > files simultaneously?
> > >
> > > > From: ayesha_comsian.hotmail.com
> > > > To: amber.ambermd.org
> > > > Date: Tue, 19 Apr 2016 14:59:01 +0500
> > > > Subject: Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file
> > > >
> > > > Dear Shahid ,
> > > > it means i have to put 4 mdcrd files instead of 1 file ?
> > > >
> > > > > From: mohammad.shahid.gmail.com
> > > > > Date: Tue, 19 Apr 2016 11:47:02 +0200
> > > > > To: amber.ambermd.org
> > > > > Subject: Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file
> > > > >
> > > > > 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 - 04:00:03 PDT
