Hi,
Hope every one is fine.
I am running an explicit water simulation using watercap with igb=10. The system contains about 11600 atoms. I have used the default values for &pb name list. Follwing is the input file.
&cntrl
imin = 1,
maxcyc = 600,
ntmin = 2,
igb = 10,
ntb = 0,
ntr = 1,
ntpr = 10,
ivcap = 0,
cut = 12
&end
&pb
maxitn = 1800
npbverb = 1
&end
Hold the ALL PROTEIN ATOMS fixed
500.0
FIND
* * * *
SEARCH
RES 1 614
END
Hold the SUGAR RING fixed
100.0
FIND
C1 * * *
C2 * * *
C3 * * *
C4 * * *
C5 * * *
O5 * * *
SEARCH
RES 618
END
END
Here, first I want to minimize the cap only so we have restrains on rest of the atoms except the sugar ring. Now the simulation fails and the output file says (an excerpt from the original file)...
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 0.0000E+00 N 1
BOND = 253.7979 ANGLE = 1866.3353 DIHED = 5598.6689
VDWAALS = 1255.2427 EEL = NaN EGB = 0.0000
1-4 VDW = 2974.2047 1-4 EEL = 25470.2433 RESTRAINT = 0.0000
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
======== FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.0000000000000
fdpb cutoff is set to 10.0000000000000
sas cutoff is set to 10.0000000000000
nonbonded cutoff is set to 10.0000000000000
Grid Constants
Grid dimension 19 19 19
Grid spacing set to 5.60000000000000
Grid boundary
-37.627 68.773
-46.838 59.562
-65.610 40.790
Dielectric Map
A single spherical dielectric boundary is used
Use probe-accessible surface definition
Compute SAS every 5 steps
Solvent probe radius 1.60000000000000
Surface dots per atom 400
Buried atom radii increment 0.800000000000000
Threshhold for exposed atom 0.200000000000000
Current SAS 0.000000000000000E+000
Boundary conditions
sum of grid charges as independent DH spheres
Physical constants
Solute dielectric constant : 1.00000000000000
Solvent dielectric constant : 80.0000000000000
Temperature (K) : 300.000000000000
Ionic strength (mM) : 0.000000000000000E+000
Debye-Huckel parameter (1/A): 0.000000000000000E+000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 1800
Convergence criteria: 1.000000000000000E-003
Iterations required : 1800
Norm of the constant vector: NaN
Norm of the residual vector: NaN
Convergence achieved : NaN
PB warning in pb_miccg(): CG maxitn exceeded!
======== FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.0000000000000
fdpb cutoff is set to 10.0000000000000
sas cutoff is set to 10.0000000000000
nonbonded cutoff is set to 10.0000000000000
Grid Constants
Grid dimension 79 79 79
Grid spacing set to 0.700000000000000
Grid boundary
-9.627 45.673
-18.838 36.462
-37.610 17.690
Dielectric Map
A single spherical dielectric boundary is used
Use probe-accessible surface definition
Compute SAS every 5 steps
Solvent probe radius 1.60000000000000
Surface dots per atom 400
Buried atom radii increment 0.800000000000000
Threshhold for exposed atom 0.200000000000000
Current SAS 0.000000000000000E+000
Boundary conditions
electrostatic focus boundary condition
Physical constants
Solute dielectric constant : 1.00000000000000
Solvent dielectric constant : 80.0000000000000
Temperature (K) : 300.000000000000
Ionic strength (mM) : 0.000000000000000E+000
Debye-Huckel parameter (1/A): 0.000000000000000E+000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 1800
Convergence criteria: 1.000000000000000E-003
Iterations required : 1800
Norm of the constant vector: NaN
Norm of the residual vector: NaN
Convergence achieved : NaN
NSTEP ENERGY RMS GMAX NAME NUMBER
10 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = 0.0000 EEL = NaN EGB = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
EAMBER = NaN
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
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NSTEP ENERGY RMS GMAX NAME NUMBER
20 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = 0.0000 EEL = NaN EGB = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
EAMBER = NaN
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB bomb in pb_reslist(): MAXNEI too short
I saw this error in the archive and there it was suggested that one should update MAXNEI manually in the pb hearder file and then recompile the code, is that recommended? similarly... if I change the cutres, cutnb and cutfd values to something smaller than default, then I recieve "maxnbr too short" error. Moreover, even if the MAXNEI thing is sloved what are these warnings all about why the iterarions all the time exceed the max value... can you spot roughly, if not clearly, what might have gone wrong and what could be done to solve it...
Any help is desperately needed and highly appreciated!
Awaiting the response...
Thanks,
Waqas.
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Received on Fri Jan 30 2009 - 01:36:47 PST
