AMBER Archive (2009)

Subject: [AMBER] Minimization error on protonated system? Please help. Thanks!

From: Haizhen Zhong (hzhong_at_mail.unomaha.edu)
Date: Thu May 28 2009 - 09:58:49 CDT

   Hello AMBER users,

   I've tried to set u small molecular binding website TUTORIAL A6.&nbs to observe the effect of duplex.
   I follo Calculations set u protonated The minimization of the neutral sytem (H atom: 0 charge and went well to the equilibration step. The +1 cha the minimization step, generated a huge energy, the below (This is for minimization of water only):
   &n GMAX & 50&n nbsp; 757
    BOND =& DIHED =&nbs VDWAALS = = &n 1-4 VDW = = 1193.4466
    EAMBER = & NSTEP &nb NAME NUMBER < 1.3642E+13 & ; = 476.1011
    VD = &nb 1-4 VDW = & RESTRAINT = 1139.5179
    EAMBER The input file is:
   initial minim &cntrl
     imin & maxcyc = 500,
     ncyc = 600 ntx = 1,
     ntc ntf = 1,
     ntb &n ntr = 1,
     cut &nb ntpr = 50,
     drms &end
   Hold the solvent fixed
   500.0 < END

   (Note: 1-22 is for DNA duplex, 23 is sma residue #24, 25-43 is Na+ to neutr
   Since the system is DNA-ligand complex, i for the neutral system (OH model, the cha this runs well). For the +1 charged with +1 charge focused on H, the partial method B) assign the charges on H the tutorials and the JACS paper on T both methods gave me the same output Any way to solve this proble Thank you very much!
   Andy Zhong

   Haizh Department of Chemistry, DSC 362
   University of Nebraska at Omaha
   6001 Dodge Street, Omaha, NE 68162
   (
   
References

   1. 3D"http://ambermd.org/tutorials_______________________________________________
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