AMBER Archive (2004)

Subject: AMBER: Problem with minimisation of an protein-inhibitor complex

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Tue Nov 23 2004 - 06:31:38 CST

Dear AMBER-users,

I have a problem performin an EM on a protein-inhibitor complex.
It is a complex of a protein (277 aa) and an inhibitor (a single aa).
The protein contains some Metal-atoms (Zn).
My problem is that if I perform an EM it seems to run endless. The last one
ran for 60000 steps wich is abnormal. If I don't fix any atom
I get an output like that or a LINMIN Failure:

MAXIMUM NUMBER OF F EVALUATION EXCEEDED
                    FINAL RESULTS
   NSTEP ENERGY RMS GMAX NAME NUMBER
  60000 -2.8572E+07 1.0475E+11 1.0596E+13 OE1 1870

 BOND = 2253.3029 ANGLE = 565.1005 DIHED =
1218.7386
 VDWAALS = 2168.2854 EEL = ************* HBOND =
0.0000
 1-4 VDW = 819.2422 1-4 EEL = 12852.7442 RESTRAINT =
0.0000

The configuration for that run looks like this :

polyA-polyT 10-mer: initial minimisation prior to MD GB model
 &cntrl
  imin = 1,
  maxcyc = 60000,
  ntmin = 2,
  dx0 = 0.1,
  dxm = 1.0,
  cut = 9.5,
 &end
eof

To find where the structure is bad I tried to fix groups of atoms
by using iBelly. So I used the following configurations :

polyA-polyT 10-mer: initial minimisation prior to MD GB model
 &cntrl
  imin = 1,
  maxcyc = 60000,
  ntmin = 2,
  dx0 = 0.1,
  dxm = 1.0,
  cut = 8.5,
  ibelly = 1,
 &end
PROTEIN
RES 2 277
END
WATER
RES 283 3589
END
END

and got the following result :

 MAXIMUM NUMBER OF F EVALUATION EXCEEDED
                    FINAL RESULTS
   NSTEP ENERGY RMS GMAX NAME NUMBER
  60000 -5.2097E+04 2.1099E-02 1.0440E+00 H1 10132

 BOND = 3563.3147 ANGLE = 567.2283 DIHED =
1244.4018
 VDWAALS = 7463.3712 EEL = -78616.4301 HBOND =
0.0000
 1-4 VDW = 829.2276 1-4 EEL = 12852.2934 RESTRAINT =
0.0000

So there were less problems calculating the energy but I did not get a
minimized structure.
So I thought it could help to perform an MD because I assumed the complex
could stick an a local minimum and got the following :
.
.
 vlimit exceeded for step 40; vmax = 1.32912849E+14
 vlimit exceeded for step 41; vmax = 1.10446189E+13
 vlimit exceeded for step 42; vmax = 7.04650286E+13
 vlimit exceeded for step 43; vmax = 2.13182016E+12
 Frac coord min, max: 0.00643121772 1.00398667
 The system has extended beyond
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

My questeions to the community are :

Is it a good method to fix groups of atoms to find "ill" regions of my
complex ?
What would you do in my case ?
Do I have a big bug within my configuration files ?

Hope anyone can help.

Best wishes,

Daniel Wetzler
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