AMBER Archive (2005)

Subject: AMBER: NAN errors

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Tue Jan 25 2005 - 15:39:45 CST

Hi All,

I am trying to minimize a protein structure with and without the presence
of water

First i tried in the presence of water and everything went fine. But when
I try to do the same without water the simulation gives the following
output

--------------------------------
   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 nan nan 1.2155E+02 O 2351

 BOND = 1307.4974 ANGLE = 3088.3520 DIHED = 4822.5876
 VDWAALS = 1321392.7282 EEL = -76345.8040 EGB = nan
 1-4 VDW = 3348.7754 1-4 EEL = 42319.0282 RESTRAINT = 0.0000
-----------------------------------

The mails in the amber mail archive say the above problem could be because
of overlapping atoms, but in my case the simulation went fine in the
presence of water so i was wondering if there is something else that i am
missing.

Below is my input file for minimization without water

-------------------

 &cntrl
        imin = 1,
        maxcyc = 5000, ncyc = 2000, ntmin = 2,
        scee = 1.2,
        nsnb = 25, cut = 8.0,
        ntpr = 100, ntwx = 100, ntwv = 100, ntwe = 100,
        ntb = 0, igb = 1,
        lastist = 7500000, lastrst = 7500000,
 &end
----------------------

Can somebody please advice me here. Thanks in advance

-Venkat

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