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.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.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.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.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
> >> > _______________________________________________
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> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
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> >
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Received on Wed Feb 04 2009 - 01:30:39 PST
