Dear Dr. Ray Luo,
I fixed fillratio to 2.0 in mm_pbsa.createinput script and in the same script space = 0.75 and varied it till 1.5 with increments of 0.25..there were two places in the script where i had to set the value for space...
i started with space = 0.75 then 1.0 then 1.25 , then 1.50..
the output messages are messages are pasted below...
however the errors were similar in all cases but when space was set to 1.5:
the error was:
"vertex atom mismatch
atom: 1291
vertex atom:1289"
1. when space = 0.75:
Grid dimension at level 1 71 55 71
Grid origin corrected at level 1 -73.500 -37.500 -48.750
Grid dimension at level 2 299 229 295
Grid origin corrected at level 2 -21.750 3.375 3.750
PB bomb in pb_setgrd(): Allocation aborted 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 41 0
0 0 0
2. when space = 1.0:
SA surface: setting up working radii
SA surface: found nonzero radii 3777
Number of SA srf points exposed455488
SA Bomb in sa_arc(): Allocation aborted 0 0 41
0 0
3. when space = 1.25:
Grid origin corrected at level 1 -125.625 -145.000 -102.500
Grid dimension at level 2 255 279 221
Grid origin corrected at level 2 -45.625 -62.500 -36.875
SA surface: setting up working radii
SA surface: found nonzero radii 3777
Number of SA srf points exposed820180
SA Bomb in sa_arc(): Allocation aborted 0 0 41
0 0
4. when space = 1.50:
FDPB Summary ========
Do FDPB every 1 steps
Nonbonded Update
residue cutoff is set to 12.000
fdpb cutoff is set to 5.000
sas cutoff is set to 9.000
nonbonded cutoff is set to 0.000
Grid Constants
Grid dimensions: 63 61 57
Grid spacing set to 6.000
Grid boundary
-156.750 221.250
-152.250 213.750
-126.750 215.250
Dielectric Map
Cavity radii in the prmtop file are used
Use probe-accessible surface definition
Compute SAS every 1 steps
Solvent probe radius: 1.400
Surface dots per atom 366
Buried atom radii increment 0.800
Threshhold for exposed atom 0.200
Current SAS ********
Boundary conditions
sum of grid charges as independent DH spheres
Physical constants
Solute dielectric constant : 1.000
Solvent dielectric constant : 80.000
Temperature (K) : 300.000
Ionic strength (mM) : 0.000
Debye-Huckel parameter (1/A): 0.000
FD Solver Option
Use Modified ICCG solver
Iteration data
Maximum iterations : 1000
Convergence criteria: 0.001
Iterations required : 38
Norm of the constant vector: 0.15507E+05
Norm of the residual vector: 0.15175E+02
Convergence achieved : 0.97860E-03
PB Warning in epsbnd(): No neighbor found for boundary grids total: 87
Vikas Sharma (+91-9780449303)
Molecular Modeling lab.
Department of Medicinal Chemistry
National Institute of Pharmaceutical Education & Research (NIPER),
SAS Nagar, Mohali,
Punjab (INDIA)
________________________________
From: Ray Luo <ray.luo.uci.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 8 June, 2009 12:47:30 AM
Subject: Re: [AMBER] Error in MM PBSA
Fix fillratio = 2 AND set space=0.75, 1.00, 1.25, and so on until the error message goes away.
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
>
Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 09 2009 - 01:12:32 PDT
