AMBER Archive (2007)

Subject: AMBER: error in modified PNA -DNA simulation..

From: Sharad gupta (sharadguptaacbr_at_yahoo.co.in)
Date: Wed Oct 10 2007 - 05:39:07 CDT


   Dear Amber user:
  I am trying to simulate modified PNA- DNA .
  PNA ( in which the whole phosphodiester backbone of DNA is replaced with 2-Aminoethylglycine backbone.)
  Modified PNA (adenine base is also modified ).
   
  I have stuck with an error
   
   Id.so.1: sander: fatal: libsunperf .so. 2: open failed No such file or directory
  /opt/age/default/spool/tentacle6/job_scripts/1101: line 5: 10035 killed
  $AMBERHOME/exe/sander ľo -i wat_nsd_md3.in -o wat_nsd_md3.out -p wat_nsd.prmtop -c wat_nsd_md2.rst -r wat_nsd_md3.rst -ref wat_nsd_md2.rst -x wat_nsd_md3.mdcrd
  gzip: wat_nsd_md3.mdcrd: no such file or directory
   
   
  My input file wat_nsd_md3.in is
   
  nsd 15-mer: 10ps MD with res(10.0) on nsd
  &cntrl
      imin = 0,
      irest = 0,
      ntx = 1,
      ntb = 1,
      cut = 10,
      ntr = 1,
      ntc = 2,
      ntf = 2,
      tempi = 0,
      temp0 = 300.0,
      ntt = 3,
      gamma_ln = 1,
      nstlim = 5000, dt = 0.002,
      ntpr = 250, ntwx = 250, ntwr = 10000
     /
  Hold the nsd fixed
  10.0
  RES 1 16
  END
  END
   
   
  Charges on PNA backbone taken from reference JACS, 1998, 120, 5895-5904
    
  But the charge on modified base is calculated from gaussian (03W).
  
   
  I have got reliable results in case of normal PNA-DNA simulation with the same input files.
   
   
  any body help me why this is happened in case of modified PNA.
   
  Thanks

       
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