Hi,
The issue is that you're attempting to execute xmgrace prior to the
actual trajectory processing run, so 02_03.rms is not generated and
the command fails. Just remove the 'xmgrace' command from your input
script and things should work.
I should probably disable those kinds of commands when cpptraj is not
being run interactively.
-Dan
On Sat, Nov 3, 2018 at 10:50 AM simon chapman <rowanlodge19.gmail.com> wrote:
>
> Hello Daniel, thank you for the prompt reply.
>
> I'm using cpptraj V17.00 and AMBER16
>
> The command is: (..$) cpptraj -p prmtop -i rmsd.cpptraj &> cpptraj.log
> Where the rmsd.rms script is: trajin 02_Heat.mdcrd
>
>
>
> trajin 03_Prod.mdcrd
>
>
>
> reference 01_Min.rst
>
>
>
> autoimage
>
>
>
> rms reference mass out 02_03.rms time 2.0 :0
>
>
>
>
>
>
> Followed by (..$) xmgrace 02_03.rms
>
> This prompts the reply " Can't stat file 02_03.rms" and obviously no
> 02_03.rms file appears in my working directory. I've tried this quite a
> few times now, with the same result. I'm baffled why it worked at the first
> attempt to follow Tutorial B0, but has failed on every occasion since...
>
> Best wishes Simon
>
>
>
>
> On Sat, 3 Nov 2018 at 13:42, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > What version of cpptraj are you using, what is your exact cpptraj input and
> > what output do you get?
> >
> > -Dan
> >
> > On Sat, Nov 3, 2018 at 5:08 AM simon chapman <rowanlodge19.gmail.com>
> > wrote:
> >
> > > Hello. I successfully followed Tutorial B0 (MD simulation of a simple
> > > dipeptide), and obtained Temp, Energy, RMSD plots. Very pleased.
> > >
> > > But, running the same simulation again, the cpptraj script wouldn't
> > produce
> > > an 02_03.rms flie. Consequently, no plots possible.
> > >
> > > I tried simulations with two other molecules (1kf1.pdb and 1fsc.pdb).
> > Both
> > > ran successfully, producing all the expected files, but again, no
> > 02_03.rms
> > > file showing after the cpptraj script command.
> > >
> > > I'm reasonably computer-literate, but not 100% IT background: I'm a
> > > molecular biologist, not a mathematician!
> > >
> > > Thanks in advance for any help Simon
> > > _______________________________________________
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> > >
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> >
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Received on Mon Nov 05 2018 - 07:00:03 PST
