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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Received on Tue Nov 23 2004 - 12:53:00 PST
