AMBER Archive (2004)

Subject: AMBER: gibbs termination

From: Carsten Detering (detering_at_u.washington.edu)
Date: Wed Apr 14 2004 - 14:17:29 CDT

Hi all,

I am using Gibbs to determine deltadeltaG values for a ligand in a
binding pocket. I performed a production run over 1ns with sander8, and
I used this as my input file:

production run with shake and PME
&cntrl

imin = 0

irest = 0

nstlim = 500000

dt = 0.002

ntx = 1

ntt =1, tempi = 300.0, temp0 = 300.0
ntc = 2, ntf = 2, tol = 0.00001
iwrap =1
scee = 1.2, scnb = 2.0
nscm = 1000
ntp = 1, pres0 = 1

ntb = 2

ntpr = 1

ntwx = 500
ntwv = 500

&end

and this is the result of the last step:

  NSTEP = 500000 TIME(PS) = 1019.000 TEMP(K) =299.73 PRESS = 305.9
  Etot = -63506.5613 EKtot =17419.5551 EPtot = -80926.1163
  BOND = 864.0087 ANGLE = 2471.8473 DIHED = 3277.2654
  1-4 NB = 1068.2128 1-4 EEL = 11646.7813 VDWAALS = 8378.9045
  EELEC = -108633.1363 EHBOND = 0.0000 RESTRAINT = 0.0000
  EKCMT = 7024.9388 VIRIAL =5189.2159 VOLUME = 277933.3957
                                             Density = 1.0395

As far as I can tell, this looks ok.

Now, for gibbs (from amber7), I use this as an input file:
gibbs input, namelist format
  &cntrl
   ntx = 1,
   ntb = 2,
   ntp = 1,
   ntt = 5,
   temp0 = 300.0,
   dt = 0.001,
   nstlim = 1000,
   nstmeq = 300,
   nstmul = 700,
   ntc = 2, ntf = 2,
   intprt=1,
   nsnb = 5,
   scnb = 2.0, scee = 1.2,
   ntpr = 50,
   nrun = 11,
   almda = 1.0,
   almdel = 0.1,
   isldyn = -3,
   ielper = 0,
  &end

  First I encountered problems with the formatted read in (ntx=7, as
after an MD run with constant pressure and periodic boundaries): Gibbs
terminated with the error
Input/Output Error 140: Invalid integer

    In Procedure: getcor
         At Line: 2187

       Statement: Formatted READ
            Unit: 9
    Connected To: state500.crd
            Form: Formatted
          Access: Sequential
Records Read : 2
Records Written: 0

Current I/O Buffer:

   49.611 36.044 53.725 49.781 35.053 53.817 49.715 36.489
54.626 50.569
     !

Does this mean, it has no velocity info? I picked one specific frame
from the produciton run (using VMD), how can I get the velocity info for
this particular frame?
As a qick and dirty method, I used ntx =1. Then gibbs runs for a while,
but stops after 150 steps (although the process is still active), and
the output file looks like this:

  Warning (EPHI): phase angle not 0 or 180 for torsion:
8106-8115-****-**** N= 2.0000 Phi= -2.9217

  NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.000 PRESS = 433.67
  Etotal = -70809.78005 Kinetic = 0.00000 Potential = -70809.78005
  Bond = 875.04771 Angle = 2478.09777 Dihed = 3267.12909
  1-4 VdW = 1066.47484 1-4 Elec= 11648.89120 Van d Waal = 8516.23958
  Elect. = -98661.66023 H-bond = 0.00000 Constraint = 0.00000
  Ekcmt = 0.00000 VirT = -3358.96389 Volume = 358731.07559
                                                  Density = 0.80535
      NSTEP = 50 TIME(PS) =0.050 TEMP(K) = 200.143 PRESS = -1469.68
  Etotal = -69258.44905 Kinetic =11633.21314 Potential = -80891.66219
  Bond = 540.39884 Angle =1608.00696 Dihed = 3053.39532
  1-4 VdW = 1085.91398 1-4 Elec=11792.22084 Van d Waal = 7557.27995
  Elect. = ************ H-bond = 0.00000 Constraint = 0.00000
  Ekcmt = 3858.22529 VirT = 15033.45474 Volume = 352172.16317
  T_solute= 180.77763 T_solvnt= 205.04366 Density = 0.82034

  Current Lambda = 1.000000
  Last F.E. update: Lambda = 1.000000 Step = 0 Method =
T.I.
  Accumulated "forward" quantities (Regular)
     Lambda = 1.000000 F_energy = 0.00000
     (Note: values are unchanged from last report)
 
------------------------------------------------------------------------------

  NSTEP = 100 TIME(PS) =0.100 TEMP(K) = 227.542 PRESS = 84.90
  Etotal = -68043.49641 Kinetic =13225.74366 Potential = -81269.24007
  Bond = 720.53187 Angle =1755.21734 Dihed = 3081.27810
  1-4 VdW = 987.79406 1-4 Elec=11678.36278 Van d Waal = 9676.22161
  Elect. = ************ H-bond = 0.00000 Constraint = 0.00000
  Ekcmt = 5134.41107 VirT = 4491.70968 Volume = 350589.55755
  T_solute= 190.50211 T_solvnt= 236.91445 Density = 0.82405

  Current Lambda = 1.000000
  Last F.E. update: Lambda = 1.000000 Step = 0 Method =
T.I.
  Accumulated "forward" quantities (Regular)
     Lambda = 1.000000 F_energy = 0.00000
     (Note: values are unchanged from last report)
 
------------------------------------------------------------------------------

  NSTEP = 150 TIME(PS) = 0.150 TEMP(K) = 242.537 PRESS = 65.79
  Etotal = -67104.52741 Kinetic = 14097.30572 Potential = -81201.83312
  Bond = 676.58073 Angle = 1882.73361 Dihed = 3102.37445
  1-4 VdW = 1039.01444 1-4 Elec= 11719.11836 Van d Waal = 9653.73150
  Elect. = ************ H-bond = 0.00000 Constraint = 0.00000
  Ekcmt = 5760.19688 VirT = 5261.39045 Volume = 351130.00538
  T_solute= 200.00535 T_solvnt= 253.29876 Density = 0.82278

Could anyone please give me some hints on what the problem is?

Thanks a lot in advance,

Carsten 

-- 

Carsten Detering
University of Washington
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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