hallo..

some clarifications and questions about this script

in the mm-pbsa script...let y = maxi @y ?ymaxset z ?zmin, -- seems ?ymaxset is not a substitution parameter. is this ?ymax set z ?zmin ?
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the deleted water residues (delete atom sele resn tip3 end) is causing atom miss match with the trajectory loop

(output file)
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CHARMM>

CHARMM> coor copy comp
SELECTED COORDINATES COPIED TO THE COMPARISON SET.


CHARMM>

CHARMM> delete atom sele resn tip3 end
SELRPN> 55719 atoms have been selected out of 60231

Message from MAPIC: Atom numbers are changed.

Message from MAPIC: 18573 residues deleted.

Message from MAPIC: 2 segments deleted.
DELTIC:55719 bonds deleted
DELTIC:18573 angles deleted
DELTIC:18573 acceptors deleted
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 5 Number of residues = 301
Number of atoms = 4512 Number of groups = 1276
Number of bonds = 4503 Number of angles = 8166
Number of dihedrals = 12012 Number of impropers = 598
Number of HB acceptors = 479 Number of HB donors = 473
Number of NB exclusions = 0 Total charge = -0.00000

CHARMM> define solute sele .not. resn tip3 end
SELRPN> 4512 atoms have been selected out of 4512

CHARMM>

CHARMM> open unit 51 read unform name /big/konidala/mpijobs/mpijob1.trj
VOPEN> Attempting to open::/big/konidala/mpijobs/mpijob1.trj::
OPNLGU> Unit 51 opened for READONLY access to /big/konidala/mpijobs/mpijob1.trj

CHARMM> open unit 52 read unform name /big/konidala/mpijobs/mpijob1_1ns.trj
VOPEN> Attempting to open::/big/konidala/mpijobs/mpijob1_1ns.trj::
OPNLGU> Unit 52 opened for READONLY access to /big/konidala/mpijobs/mpijob1_1ns.trj

CHARMM>

CHARMM> ! Get trajectory file parameters
CHARMM> !traj iread 51
CHARMM>

CHARMM> ! MM-PBSA Analysis
CHARMM> ! For Emm, dGpb, dGasa calculation, analyze 10 ps snapshots
CHARMM> ! For quasiharmonic analysis, use full trajectory with 100 fs skip
CHARMM>

CHARMM> traj iread 51 nunits 2 skip 500
TRAJ: INITIATING READ OF A TRAJECTORY, OPTIONS;
FIRSTU = 51 NUNIT = 2 SKIP = 500

CHARMM>

CHARMM> set a 10
Parameter: A <- "10"

CHARMM> set b 10
Parameter: B <- "10"

CHARMM> !calc z = 300 * 2
CHARMM>

CHARMM> set dcel 0.40 ! Grid spacing variable for PB equaition solution
Parameter: DCEL <- "0.40"

CHARMM>

CHARMM> ! MM-PBSA equiation
CHARMM> ! G = + + - TdS
CHARMM> set emm 0 ! Solute internal energy
Parameter: EMM <- "0"

CHARMM> set inte 0 ! ENER - VDW - ELEC
Parameter: INTE <- "0"

CHARMM> set exte 0 ! VDW + ELEC
Parameter: EXTE <- "0"

CHARMM> set dgpb 0 ! solvation free energy from finite diffrence PB eq
Parameter: DGPB <- "0"

CHARMM> set dgasa 0 ! nonpolar contribution to solvation free energy
Parameter: DGASA <- "0"

CHARMM> set n 0 ! snapshot counter
Parameter: N <- "0"

CHARMM>

CHARMM> nbonds ! set up nonbond list (defaults from parameter set used)

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
<MAKINB> with mode 5 found 12669 exclusions and 11780 interactions(1-4)
<MAKGRP> found 3459 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 1296530 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
1207447 ATOM PAIRS WERE FOUND FOR ATOM LIST
67169 GROUP PAIRS REQUIRED ATOM SEARCHES


CHARMM>

CHARMM> label trajloop

CHARMM> traj read

READING TRAJECTORY FROM UNIT 51
NUMBER OF COORDINATE SETS IN FILE: 1120
NUMBER OF PREVIOUS DYNAMICS STEPS: 40500
FREQUENCY FOR SAVING COORDINATES: 500
NUMBER OF STEPS FOR CREATION RUN: 560000

***** ERROR ***** NO. OF ATOMS DO NOT MATCH 4512 60231
*** LEVEL -4 WARNING *** BOMLEV IS -2
BOMLEV HAS BEEN SATISFIED. TERMINATING.

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commenting the line.. delete atom sele resn tip3 end in the script and considering the whole system, the job terminates with the warning from VEHEAP storage request. eventhough i am using a higher heap size of 40480000.


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CHARMM>

CHARMM> pbeq

Calculations with the Poisson-Boltzmann Equation


PBEQ> scalar wmain = radius

PBEQ>

PBEQ> solve dcel @dcel nclx @xcel ncly @ycel nclz @zcel maxit 1000 -
PBEQ> epsw 80.0 epsp 4.0 temp 298 watr 1.4 intbp
Parameter: DCEL -> "0.40"
Parameter: XCEL -> "252"
Parameter: YCEL -> "252"
Parameter: ZCEL -> "220"

Calculation with 60231 atoms

LINEARIZED PBEQ SOLVER: Successive OverRelaxation (SOR) method

ITERATION PARAMETERs
Maximum # iterations (MAXITS) = 1000
Tolerance of convergence (DEPS) =.200E-05
Mixing factor (LAMBDA,DOME) = 1.000

CHARGE DISTRIBUTION METHOD: the trilinear interpolation

BOUNDARY POTENTIAL CALCULATION METHOD
The Debye-Huckel approximation for half number of boundary points along 1d-axis and
potential of the rest will be interpolated from nearest grid points

PHYSICAL PARAMETERs
Solvent probe radius (WATR) = 1.400 [Angs]
Ion exclusion radius (Stern layer) = 0.000 [Angs]
Solvent dielectric constant (EPSW) = 80.000
Protein dielectric constant (EPSP) = 4.000
Salt concentration (CONC) = 0.000 [moles]/[liter]
Temperature (TEMP) = 298.000 [K]
Debye-Huckel factor (KAPPA2) = 0.000 [1/Angs**2]

NUMBER OF GRID POINTS: 253 253 221
Box in X from -50.400 to 50.400
Box in Y from -50.400 to 50.400
Box in Z from -44.000 to 44.000
VEHEAP> Expanding heap size by14155776 words.
VEHEAP> Expanding heap size by14155776 words.
VEHEAP> Error: MALLOC returned ZERO.

***** LEVEL -4 WARNING FROM <VEHEAP> *****
***** COULD NOT SATISFY STORAGE REQUEST.
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5

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will this PBEQ method work for randomly distributed lipids and ions around the protein without deleting them for the free energy calculations?


thanks for your comments in advance.

cheers