Tue Oct 11 06:00:17 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:00:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2020 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7062511 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 0.7062511 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1919 net assigned charge : 5.931010 assigned positive charge : 312.7391 centred at (gu) : 89.07812 89.17825 90.47366 assigned negative charge : -306.8082 centred at (gu) : 88.94646 89.19559 90.53815 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6878 nv = 96 ne = 84 npr = 39729 no. pairs analyzed = 39729 no. exposed pairs = 2498 no. arc points = 17169 no. surface atoms = 850 nbur = 1170 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3896 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1622 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2720290E-08 2.0249814E-08 midg,1,midg; midg,igrid,midg 6.7329310E-08 3.5347167E-08 1,midg,midg; igrid,midg,midg -1.7139687E-08 9.2674071E-08 gauss-seidel spectral radius is 0.9895443 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 06:00:17 rms-change max change #iterations 0.1968202 26.68068 at 10iterations 2.4584835E-02 3.516739 at 20iterations 3.1548410E-03 0.4979019 at 30iterations 4.5731649E-04 6.4977646E-02 at 40iterations 9.4155497E-05 1.4595032E-02 at 50iterations finished qdiffx linear iterations at : 06:00:20 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 9.4155497E-05 1.4595032E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:00:21 3.314u 0.164s 0:03.96 87.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:00:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2020 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118753 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 2.118753 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1919 net assigned charge : 5.931010 assigned positive charge : 312.7391 centred at (gu) : 87.23436 87.53462 91.42096 assigned negative charge : -306.8082 centred at (gu) : 86.83957 87.58666 91.61451 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 29290 mr = 51546 m= 5720 mr = 22256 m= 495 mr = 3714 m= 8 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15232 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7062511 object centre at (A) : 3.746500 9.273001 22.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7562594E-02 6.1068993E-02 midg,1,midg; midg,igrid,midg 3.0176416E-02 3.1101655E-03 1,midg,midg; igrid,midg,midg 2.2016319E-02 3.2466143E-02 gauss-seidel spectral radius is 0.9988227 estimated iterations to convergence 231 setup time was (sec) 0.5800000 now iterating at: 06:00:22 rms-change max change #iterations 4.551281 184.0734 at 10iterations 2.255056 76.88278 at 20iterations 1.111780 34.50541 at 30iterations 0.5513254 17.88469 at 40iterations 0.2741199 8.560365 at 50iterations 0.1353708 4.357529 at 60iterations 6.7083500E-02 1.974800 at 70iterations 3.3269819E-02 1.059357 at 80iterations 1.6543455E-02 0.5077941 at 90iterations 8.2345549E-03 0.2759476 at 100iterations 4.1008797E-03 0.1351213 at 110iterations 2.0873086E-03 6.5886021E-02 at 120iterations finished qdiffx linear iterations at : 06:00:29 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.0873086E-03 6.5886021E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 06:00:29 7.676u 0.186s 0:08.43 93.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:00:29 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2020 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.178130 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -19.89600 27.38900 ymin,ymax (A): -9.967999 28.51400 zmin,zma (A): -3.192000 47.21500 x,y,z range (A): 47.28500 38.48200 50.40700 scale (grids/A): 3.178130 object centre (A): 3.746500 9.273001 22.01150 number of atom coordinates read : 2020 total number of charged atoms : 1919 net assigned charge : 5.931010 assigned positive charge : 312.7391 centred at (gu) : 85.85162 86.30191 92.13140 assigned negative charge : -306.8082 centred at (gu) : 85.25932 86.38004 92.42188 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 168054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 91391 mr = 123963 m= 37415 mr = 76166 m= 10689 mr = 30539 m= 2098 mr = 8191 m= 244 mr = 1544 m= 3 mr = 145 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 69344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 15352 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.118753 object centre at (A) : 3.746500 9.273001 22.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2960783 0.9161496 midg,1,midg; midg,igrid,midg 0.2442131 -6.0744011E-03 1,midg,midg; igrid,midg,midg 0.3861995 0.2765226 gauss-seidel spectral radius is 0.9992943 estimated iterations to convergence 297 setup time was (sec) 1.350000 now iterating at: 06:00:31 rms-change max change #iterations 10.20969 480.8877 at 10iterations 6.035088 122.1423 at 20iterations 3.548465 74.03696 at 30iterations 2.090843 38.00974 at 40iterations 1.228307 25.08658 at 50iterations 0.7201534 12.61766 at 60iterations 0.4221672 8.143211 at 70iterations 0.2473527 4.460571 at 80iterations 0.1446871 2.577191 at 90iterations 8.4620818E-02 1.496243 at 100iterations 4.9623087E-02 0.8603745 at 110iterations 2.9121103E-02 0.5803070 at 120iterations 1.7212933E-02 0.2948055 at 130iterations 1.0270106E-02 0.1928787 at 140iterations 6.2321671E-03 0.1240253 at 150iterations 3.8623635E-03 7.2462082E-02 at 160iterations 2.5120154E-03 4.4441223E-02 at 170iterations 1.7227518E-03 3.4568787E-02 at 180iterations finished qdiffx linear iterations at : 06:00:42 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 1.7227518E-03 3.4568787E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 06:00:43 12.579u 0.201s 0:13.31 95.9% 0+0k 0+0io 0pf+0w