AMBER Archive (2009)

Subject: [AMBER] MM-PBSA tutorial

From: Workalemhu Berhanu (wberhanu_at_mail.ucf.edu)
Date: Thu May 14 2009 - 12:16:55 CDT

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

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