AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA tutorial

From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Thu May 14 2009 - 20:19:04 CDT

Check your environment variables. If you did not set
$AMBERHOME=youramberdir, PBS gives errors like that.

On Thu, 2009-05-14 at 13:26 -0400, steinbrt_at_rci.rutgers.edu wrote:
> Hi,
>
> the error means that sander did not find the file heat.rst which is an
> input coordinate file. It is supposed to be the output of a previous
> sander run.
>
> You know that the various minimization, equilibration and production steps
> need to be run sequentially, not all at once, right? Otherwise, check the
> output .out file from the very first job you run to see why it did not
> provide a restart file, it probably crashed for some reason.
>
> Kind Regards,
>
> Thomas
>
> On Thu, May 14, 2009 1:16 pm, Workalemhu Berhanu wrote:
> > Dear all,
> > I am new user to amber. I was doing the tutorial on amber web site for
> > free energy calculation (amber advanced tutorials tutorial 3 MM-PBSA)
> > using amber9 version. I build the starting structure and the files I get
> > at this stage (the files: ras-raf.prmtop, ras-raf.inpcrd, ras.prmtop,
> > ras.inpcrd, raf.prmtop, raf.inpcrd, ras-raf_solvated.prmtop,
> > ras-raf_solvated.inpcrd) are the same as in the tutorial. I used the input
> > files (min.in, heat.in, density.in and equil.in) and then I run all run
> > all 4 of these simulations using commands along the lines in the tutorial.
> > When I vi equil.pbs.e35560. ---
> > I got this
> > /var/spool/pbs/mom_priv/jobs/35560.emgnt1.SC: line 13:
> > AMBERHOME/exe/sander: No such file or directory
> >
> > Unit 30 Error on OPEN: heat.rst
> > /var/spool/pbs/mom_priv/jobs/35560.emgnt1.SC: line 17:
> > AMBERHOME/exe/sander: No such file or directory
> > Can somebody help me fixing this problem?
> >
> > Regards
> >
> > Workalemahu
> > Department of chemistry
> > University of Central Florida
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student @ Schiffer Lab

364 Plantation St. LRB 970M
Worcester, MA 01605

cihan.aydin_at_umassmed.edu
+1 (508) 856-3430

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