Your version is quite old, try to upgrade to ambertools 17.
Hai
On Tue, Dec 19, 2017 at 9:32 AM Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
>
> Hi Dan,
> Thank you very much. I follow the manual and command the you have
> referred. But I got the following error during processing my rem log file.
> It is not generating the output file 'accept.dat'. Please suggest what to
> do.
>
> CPPTRAJ: Trajectory Analysis. V14.25
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> > readdata test-rem.log as remlog
> Reading 'test-rem.log' as Amber REM log with name 'test-rem.log'
> Reading from log files: test-rem.log
> 32 Hamiltonian replicas.
> Initial H-REMD coordinate indices: 1 2 3 4 5 6 7 8 9 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
> test-rem.log should contain 340 exchanges
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> <runanalysis remlog test-rem.log out trepidx.agr repidx name acceptout
> accept.dat
> REMLOG: test-rem.log, 32 replicas, 340 exchanges
> Getting replica index vs exchange.
> Output is to trepidx.agr
> Error: [remlog] Not all arguments handled: [ acceptout accept.dat ]
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
> TIME: Total analysis execution time: 0.0070 seconds.
>
>
>
> > -----Original Messages-----
> > From: "Daniel Roe" <daniel.r.roe.gmail.com>
> > Sent Time: 2017-12-19 02:50:19 (Tuesday)
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Cc:
> > Subject: Re: [AMBER] HREMD run
> >
> > See the Amber 17 manual, 28.10.25. remlog (page 670-671) for command
> > syntax, details, and examples.
> >
> > -Dan
> >
> > On Mon, Dec 18, 2017 at 6:28 AM, Dr. MANAS MONDAL <manas.pku.edu.cn>
> wrote:
> > >
> > > What is the syntax for 'remlog' analysis command in cpptraj and how I
> will run it using my rem.log file ?
> > >
> > > Manas
> > >
> > >> -----Original Messages-----
> > >> From: "Daniel Roe" <daniel.r.roe.gmail.com>
> > >> Sent Time: 2017-12-15 22:38:10 (Friday)
> > >> To: "AMBER Mailing List" <amber.ambermd.org>
> > >> Cc:
> > >> Subject: Re: [AMBER] HREMD run
> > >>
> > >> Hi,
> > >>
> > >> Exchange acceptance is printed in the HREMD log, the very last column.
> > >>
> > >> You can also use the 'remlog' analysis command from cpptraj to
> > >> calculate the exchange acceptance from 1 or more rem logs.
> > >>
> > >> -Dan
> > >>
> > >>
> > >> On Thu, Dec 14, 2017 at 8:47 PM, Dr. MANAS MONDAL <manas.pku.edu.cn>
> wrote:
> > >> > Hi,
> > >> > Please let me help by giving me the information about how can I
> calculate the Exchange acceptance ratio from the output log file (rem.log)
> of the HREMD run. I am waiting for your response.
> > >> > Thanking you.
> > >> > Manas
> > >> > _______________________________________________
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> > >> > AMBER.ambermd.org
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> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe
> > >> Laboratory of Computational Biology
> > >> National Institutes of Health, NHLBI
> > >> 5635 Fishers Ln, Rm T900
> > >> Rockville MD, 20852
> > >> https://www.lobos.nih.gov/lcb
> > >>
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> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Dec 18 2017 - 19:00:05 PST
