AMBER Archive (2002)

Subject: EGB = NaNQ

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Thu Oct 03 2002 - 16:05:55 CDT

I am having problems with a gas phase minimization run. Few hydrogen atoms placed by
leap are making close contact with other atoms. To remove these contacts I am
performing a minimization run. The run fails after few steps.The output file shows "EGB
= NaNQ" at the first step. I was wondering what the problem could be and what does this
term corresponds to?
(Interestingly, this problem does not show when I solvate the system with explicit
water and run the minimization step).

Is this problem related to 'saltcon' keyowrd? Any help will be really appreciated.

Some information:

System type : Protein-DNA complex
Gas phase : Yes (igb=1; ntb=0)
Counter ions: Yes (20 Na+ ions)
AMBER : 7.0
Platform : IBM AIX5.1
Parallel : Yes (8 cpus)

Input 

----
 &cntrl
     imin=1, maxcyc=50000, ntmin=1, igb=1,
     cut=8.0, drms=0.001, nsnb=10, ntb=0,
     ntc=1, ntf=0, ntr=1, ntpr=5,
 &end
----

Output (part) 
---
  NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1             NaNQ          -NaNQ     0.0000E+00     N           1

 BOND    =      381.3432  ANGLE   =     1584.6041  DIHED      =     1966.7790
 VDWAALS = *************  EEL     =   -27157.4566  EGB        =          NaNQ
 1-4 VDW =     1680.5651  1-4 EEL =    11063.3929  RESTRAINT  =        0.0000

   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      5            -NaNQ          -NaNQ     0.0000E+00     N           1
      
 BOND    =         -NaNQ  ANGLE   =  2184741.0631  DIHED      =     1002.2800
 VDWAALS =         -NaNQ  EEL     =         -NaNQ  EGB        =         -NaNQ
 1-4 VDW =         -NaNQ  1-4 EEL =         -NaNQ  RESTRAINT  =        0.0000
      
      
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
     10            -NaNQ          -NaNQ     0.0000E+00     N           1
      
 BOND    =         -NaNQ  ANGLE   =  2184741.0631  DIHED      =     1002.2800
 VDWAALS =         -NaNQ  EEL     =         -NaNQ  EGB        =         -NaNQ
 1-4 VDW =         -NaNQ  1-4 EEL =         -NaNQ  RESTRAINT  =        0.0000
      
     .... RESTARTED DUE TO LINMIN FAILURE ...
      
   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
     15            -NaNQ          -NaNQ     0.0000E+00     N           1
      
 BOND    =         -NaNQ  ANGLE   =  2184741.0631  DIHED      =     1002.2800
 VDWAALS =         -NaNQ  EEL     =         -NaNQ  EGB        =         -NaNQ
 1-4 VDW =         -NaNQ  1-4 EEL =         -NaNQ  RESTRAINT  =        0.0000
------

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