AMBER Archive (2009)

Subject: [AMBER] restrained minimization

From: quantum_mania_at_yahoo.com
Date: Mon Apr 13 2009 - 19:12:35 CDT

Hi,

I wanted to minimize a system with all heavy atoms frozen, so I had the input file:

 &cntrl
  ntxo = 1,
  ntf = 1, ntb = 0,
  cut = $13,
  imin = 1, maxcyc = 500,
  ncyc = 200, drms = 0.0001,
  igb = 2, gbsa = 1,
  saltcon= 0.2,
  ntr = 1, restraint_wt=100,
  restraintmask="!@H="
 &end

The output, though, showed most atoms minimized were the heavy atoms:

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 2.4891E+06 3.5774E+05 2.8493E+07 N 2350

 BOND = 11236.9288 ANGLE = 1977.3661 DIHED = 3671.5910
 VDWAALS = 2254558.2581 EEL = -28340.6309 EGB = -2424.7008
 1-4 VDW = 231637.2474 1-4 EEL = 16749.2026 RESTRAINT = 0.0000
 ESURF = 58.0214

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 -9.7251E+03 1.5028E+00 6.8717E+01 HB 2355

 BOND = 192.4587 ANGLE = 882.4130 DIHED = 3641.6436
 VDWAALS = -2640.3375 EEL = -28426.9349 EGB = -2571.6284
 1-4 VDW = 1680.7545 1-4 EEL = 16745.9207 RESTRAINT = 713.4054
 ESURF = 57.1554
 EAMBER = -10438.5549

   NSTEP ENERGY RMS GMAX NAME NUMBER
    100 -1.0366E+04 1.0488E+00 6.0425E+01 C 2348

 BOND = 158.4953 ANGLE = 792.6656 DIHED = 3608.9566
 VDWAALS = -2763.6613 EEL = -28773.3915 EGB = -2311.5559
 1-4 VDW = 1625.8374 1-4 EEL = 16754.9857 RESTRAINT = 484.6390
 ESURF = 56.9623
 EAMBER = -10850.7057

   NSTEP ENERGY RMS GMAX NAME NUMBER
    150 -1.0546E+04 5.4551E-01 2.2807E+01 C 2348

 BOND = 148.1752 ANGLE = 770.5663 DIHED = 3580.3300
 VDWAALS = -2800.2714 EEL = -28648.9588 EGB = -2463.5062
 1-4 VDW = 1613.3656 1-4 EEL = 16753.1891 RESTRAINT = 444.3670
 ESURF = 56.9385
 EAMBER = -10990.1718

   NSTEP ENERGY RMS GMAX NAME NUMBER
    200 -1.0633E+04 1.0241E+00 5.6205E+01 C 2348

 BOND = 147.2695 ANGLE = 762.4944 DIHED = 3555.1094
 VDWAALS = -2818.1369 EEL = -28668.2087 EGB = -2459.1209
 1-4 VDW = 1607.3161 1-4 EEL = 16752.0424 RESTRAINT = 430.8578
 ESURF = 56.9773
 EAMBER = -11064.2575

Is there anything wrong with my sander input file?

Thanks!

DX
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