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 Sat Nov 03 2018 - 08:00:03 PDT
