Hi,
If you are following the tutorial, you need to make sure to reproduce it
first, which is by typing exact script command the tutorial use.
for example:
process_mdout.perl ../polyAT_vac_md1_nocut.out
in
http://ambermd.org/tutorials/basic/tutorial1/section3.htm
Hai
On Mon, Oct 17, 2016 at 12:04 AM, Stacyann Nelson <mitize2000.yahoo.com>
wrote:
> Hi
> Hai, I did not install amber I am using comet on SDSC.
> Alican, you are correct I am running from bash.
>
> Do I just type perl into the command line inorder to use the
> process_mdout.perl?
>
> On Sunday, October 16, 2016 11:58 PM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
>
>
> hi,
>
> have you installed amber by yourself?
> If you did not see any process_mdout.perl in $AMBERHOME/bin, there was
> something wrong with your installation.
> Please check installation section in amber15 manual,
> http://ambermd.org/doc12/Amber15.pdf, page 23.
>
> Follow Alican's suggestion might help to solve your issue too.
>
> Hai
>
> On Sun, Oct 16, 2016 at 11:49 PM, Stacyann Nelson <mitize2000.yahoo.com>
> wrote:
>
> > Hi Hai,
> > Thank you for your response.
> > I am using amber/15
> > I am new to molecular dynamics what do you mean by source amber.sh?
> > I have module load amber.
> > I search the bin and no perl script.
> > Regards Stacy
> >
> >
> >
> > Sent from Yahoo Mail on Android
> >
> > On Sun, Oct 16, 2016 at 11:36 PM, Hai Nguyen<nhai.qn.gmail.com> wrote:
> > hi,
> >
> > which version of amber you are using? have you sourced amber.sh yet?
> > That perl script is normally in *$AMBERHOME/bin*
> >
> > cheers
> > Hai
> >
> > On Sun, Oct 16, 2016 at 11:14 PM, Stacyann Nelson <mitize2000.yahoo.com>
> > wrote:
> >
> > > Dear All,
> > >
> > > I ran MD simulations to equilibrate a protein strand and now I would
> like
> > > to analyze the results. However using the process_mdout. perl from the
> > > tutorial is giving the following error on Comet.
> > >
> > > -bash: process_mdout.perl: command not found
> > >
> > > My question is how can I get this into my path on comet to run the
> > > analysis?
> > >
> > > Regards
> > >
> > > Stacy
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 16 2016 - 21:30:02 PDT
