AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA tutorial

Date: Thu May 14 2009 - 12:26:50 CDT


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,


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 (,, and 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

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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