AMBER Archive (2001)

Subject: minimization

From: Andrew Aird (a.aird_at_physik.uni-stuttgart.de)
Date: Tue Apr 10 2001 - 11:05:27 CDT

Dear Amber users

I've encounterd a problem while trying to minimize a solvated protein. Every
time I try to start sander, I get the following output:

#######################################################################

          -------------------------------------------------------
          Amber 6 SANDER Scripps/UCSF 1999
          -------------------------------------------------------

| Tue Apr 10 18:00:55 2001

  [-O]verwriting output

File Assignments:
|MDIN : min_solvent.in
|MDOUT: ./tri02_sol/min_sol2.out
|INPCR: /home/aa3/startstrukturen/triX_(2)_sol/tri2_sol.prmcrd
|PARM : /home/aa3/startstrukturen/triX_(2)_sol/tri2_sol.prmtop
|RESTR: ./tri02_sol/min_sol2.rstrt
|REFC : /home/aa3/startstrukturen/triX_(2)_sol/tri2_sol.prmcrd
|MDVEL: mdvel
|MDEN : mden
|MDCRD: mdcrd
|MDINF: /home/aa3/startstrukturen/triX_(2)_sol/tri2_sol.mdinfo

 Here is the input file:

 &cntrl
  imin = 1,
  ntr = 1,
  ntpr = 100,
  cut = 8.0,
  scee = 1.2,
  maxcyc = 3000,
  ncyc = 3000,
  dx0 = 0.03,
 &end
#restrain the protein
500.0
RES 1 1266
END
END
                                                                               
                                                                               
-------------------------------------------------------------------------------

 &cntrl

   1. RESOURCE USE:

 getting box info from bottom of parm
 getting new box info from bottom of inpcrd
 peek_ewald_inpcrd: SHOULD NOT BE HERE

##########################################################################################

Does anyone know what this means?

Thanks a lot for any comments...

---------------------------------------------------
Andrew Aird
3.Physikalisches Institut
Universität Stuttgart
Pfaffenwaldring 57
D 70569 Stuttgart
Tel: +49 711 685-5232
e-mail: a.aird_at_physik.uni-stuttgart.de
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