AMBER Archive (2009)

Subject: Re: [AMBER] creating a restart file from md.out

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 03 2009 - 09:34:44 CST

maybe you should work through the tutorials and make sure you can get
ptraj running before trying this.
have you run ptraj before to do any data analysis?
think carefully about what is in your files- for example, do you
really have 726000 frames in your mdcrd file?
is the mdcrd file really called equ.out?
following the tutorials will really help you since the ptraj inputs
are given and explained, and once you have done those it will be
easier to modify the scripts to do your own analysis.

I also suggest you upgrade from amber9 to the much more current
ambertools v1.2 that can be downloaded from the amber web page.

On Tue, Feb 3, 2009 at 10:29 AM, oguz gurbulak <gurbulakoguz_at_gmail.com> wrote:
> I wrote the ptraj.in and run . I got this error in below. What should I do
> to solve it ?
>
> ptraj.in
>
> trajin equ.out 726000 726000
> trajout md.rest restart
>
> ptraj n-dodecane.prmtop < ptraj.in > md.rest
>
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 9.0 integrated" (April 2006)
> -/- Executable is: "ptraj"
> /-\
> \-/ DEC DEC DEC DEC DEC DEC DEC DEC DEC DEC
> ...
>
>
> PTRAJ: Processing input from "STDIN" ...
>
> PTRAJ: trajin equ.out 726000 726000
>
> PTRAJ: trajout md.rest restart
> WARNING in ptraj(): No input trajectories specified (trajin), aborting...
>
> 2009/2/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>
>
>> why did you do the
>> >n-dodecane.rest
>> ??
>> this sends the ptrajout output to that file, overwriting the restart
>> file that you make in the trajout command.
>> send the ptraj output to a different fil;e, and make sure to read the
>> ptraj output carefully, noting any errors or warnings and make sure
>> that the output from ptraj looks like what you expect from the
>> commands that you gave. ptraj is very good about telling you what it
>> thinks you asked it to do.
>>
>>
>>
>> On Tue, Feb 3, 2009 at 8:22 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
>> wrote:
>> > I created a ptraj input file as you said and run the script writing:
>> > ptraj n-dodecane.prmtop < ptraj.in > n-dodecane.rest , but I couldn't
>> get
>> > the n-dodecane.rest file. Could you help me about it ?
>> >
>> > Thanks in advance.
>> >
>> > ptraj.in
>> >
>> > trajin n-dodecane.equ.mdcrd 726000 726000
>> > trajout n-dodecane.rest restart
>> >
>> > 2009/2/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> >
>> >> the mdout file does not have coordinate information. that is in the
>> mdcrd
>> >> file.
>> >> if you wrote to the mdcrd file at this step (if depends on your
>> >> setting of ntwx), then
>> >> you can use ptraj trajin/trajout to extract that frame to a restart
>> file.
>> >>
>> >> let's say you want to extract frame 726 (your nstep is 726000 and
>> >> perhaps you set ntwx to 1000)
>> >> then you can do this inside a ptraj script
>> >>
>> >> trajin mdout 726000 726000
>> >> trajout filename restart
>> >>
>> >> along with all of the other things needed for running ptraj, this is
>> >> just part but I assume you've already learned ptraj)
>> >>
>> >>
>> >>
>> >> On Tue, Feb 3, 2009 at 5:44 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
>> >> wrote:
>> >> > Dear All,
>> >> >
>> >> > I want to extract the output informations for NSTEP = 726000 in target
>> >> > Density =0.7636 , create a restart file for input and start a md from
>> >> this
>> >> > point with little time steps. Is
>> >> > it possible to do this in Amber ? If so, what should I do to do this
>> >> > operation ?
>> >> >
>> >> >
>> >> >
>> >> > NSTEP = 726000 TIME(PS) = 1452.000 TEMP(K) = 271.69 PRESS =
>> >> > 350.4
>> >> > Etot = 3756.1288 EKtot = 2374.7495 EPtot =
>> >> > 1381.3794
>> >> > BOND = 346.1359 ANGLE = 1656.2278 DIHED =
>> >> > 677.9015
>> >> > 1-4 NB = 456.8660 1-4 EEL = 384.6550 VDWAALS =
>> >> > -1729.3428
>> >> > EELEC = -411.0640 EHBOND = 0.0000 RESTRAINT =
>> >> > 0.0000
>> >> > EKCMT = 73.3705 VIRIAL = -206.8362 VOLUME =
>> >> > 37038.6242
>> >> > Density =
>> >> > 0.7636
>> >> > Ewald error estimate: 0.4255E-04
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER_at_ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
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