Can you post or send me the output that is in cpptraj.log? Thanks.
-Dan
On Mon, Nov 5, 2018 at 5:11 PM simon chapman <rowanlodge19.gmail.com> wrote:
>
> Hello again Dan...Sorry, might not have made the problem clear. I am
> executing the xmgrace command *after* the cpptraj command,not before.
> xmgrace isn't part of the input script.
>
> Attached screen shot shows the sequence. It does look like the cpptraj
> script isn't generating the 02_03.rms file.
>
> BW Simon
>
> On Mon, 5 Nov 2018 at 14:40, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > 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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Received on Thu Nov 08 2018 - 05:30:02 PST
