AMBER Archive (2008)

Subject: AMBER: GBSA SA calculation

From: Titus, Jamie \(bairdje\) (BAIRDJE_at_ucmail.uc.edu)
Date: Wed May 07 2008 - 13:32:43 CDT

Hello all,

I am currently trying to extract SA terms from a trajectory which I have stripped of H2O and ions, recreated the proper water/ion free prmtop, and used the following input file and command to run the calculation:

surface.in - Calculate solvent accessible surface area
 &cntrl
  imin = 5,
  gbsa = 2,
  igb = 1,
  ntb = 0,
 surften = 1,
  cut = 99,
 /

sander -O -i surface.in -p waterandionfree.prmtop -x trajectorystrippedofH2Oandions.crd -c waterionfreeoriginalcrd.crd -o surface.out

I have tried this procedure with several different trajectories of different systems, and each time I am getting the following error:

 4. RESULTS
--------------------------------------------------------------------------------

 POST-PROCESSING OF TRAJECTORY ENERGIES
 Error in trajectory file
 error in trajene()

Not sure what the problem is - didn't see it in the archive anywhere. Using serial installation of Amber9 on a Linux AMD Opteron Dualcore.

Jamie Baird-Titus
Post-Doctoral Fellow
Laboratory of Professor Mark Rance
Department of Molecular Genetics, Biochemistry, and Microbiology
University of Cincinnati College of Medicine
Rm. 3109 Medical Sciences Bldg.,
231 Albert Sabin Way, Cincinnati, OH 45267
phone:(513)558-2938
email:bairdje_at_ucmail.uc.edu
website: http://jamiebairdtitus.googlepages.com

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