AMBER Archive (2000)

Subject: docking

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Mon Oct 02 2000 - 12:15:21 CDT

Dear Colleagues,

does anybody have a complete and correct input file for docking with AMBER
5.0/6.0. My own input file looks like this

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MD production, tautp=0.2, taup=0.2
 &cntrl

   nmropt = 1, timlim = 9999000,
   ntb = 1, ntpr = 100, ntwx = 500,

   cut = 9.0,

   tempi = 298.16, temp0 = 298.16, ig=555333,
   ntt = 1, tautp = 1.0, taup = 1.0,
   ntp = 0, vlimit = 20, nsnb=10,

   imin = 0,
   nstlim = 500000, dt = 0.002,
   ntc = 3, ntf = 3, tol = 0.00001,
   nscm = 1000, ntcm = 1,
   iwrap = 1,

 &end
 &ewald
   ew_type = 0, skinnb = 1.0, nbflag = 1, use_pme = 1, vdwmeth = 1,
 &end

 &rst iat=4905,1306,
      iresid=0,
      nstep1=1, nstep2=500,
      irstyp=0, ifvari=1, ninc=0, imult=0, ir6=0, ifntyp=0, ,
      r1=0.00000, r2=13.3000, r3=13.3000, r4=99.000, rk2=1.0000,rk3=1.0000, ,
      r1a=0.00000, , r2a=5.5000, r3a=5.5000, r4a=99.000,rk2a=1.0000,rk3a=1.0000,
 &end
 &rst iat=0, &end

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but it doesn't work. Thank you for your help.

                                                        Michal Otyepka
      
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