AMBER Archive (2009)

Subject: Re: [AMBER] Error in MM PBSA

From: Ray Luo (ray.luo_at_uci.edu)
Date: Mon Jun 08 2009 - 13:12:22 CDT

So in the end, you were able to run it on your computer with space=1.50 ...

The error message on "vertex atom mismatch" is from molsurf, the surface
calculation routine. Maybe someone on the list can help you on this ...

If not, you can specify in your mmpbsa script to turn off MS and use the
surface routine in pbsa instead. Looks that the surface calculation
procedure in pbsa can handle your system ... Please carefully read the
instruction in the script on how to turn it on.

All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

Vikas Sharma wrote:
> 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_at_uci.edu>
> To: AMBER Mailing List <amber_at_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_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
>
>>
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>
>
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