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-- 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 ? > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > AMBER mailing list > > > > > > AMBER.ambermd.org > > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > _______________________________________________ > > > > > AMBER mailing list > > > > > AMBER.ambermd.org > > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Apr 19 2016 - 03:30:04 PDT