Mon Oct 10 13:59:06 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+sph.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 = amb.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 Mon Oct 10 2011 at 13:59:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6138777 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 0.6138777 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3122 net assigned charge : 4.000012 assigned positive charge : 488.9228 centred at (gu) : 92.23214 88.36886 90.39467 assigned negative charge : -484.9242 centred at (gu) : 92.23233 88.33682 90.46551 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 67339 no. pairs analyzed = 67339 no. exposed pairs = 3748 no. arc points = 26364 no. surface atoms = 1273 nbur = 1996 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 4614 m= 0 mr = 32 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 3842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2692 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9073502E-09 -2.4248588E-09 midg,1,midg; midg,igrid,midg 6.4464767E-10 3.4348813E-09 1,midg,midg; igrid,midg,midg 1.6930884E-09 4.3798600E-09 gauss-seidel spectral radius is 0.9863124 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 13:59:07 rms-change max change #iterations 0.1345554 19.27209 at 10iterations 1.2548630E-02 1.679899 at 20iterations 1.2391728E-03 0.1574783 at 30iterations 1.5929760E-04 2.1389008E-02 at 40iterations 3.0855455E-05 4.8217773E-03 at 50iterations finished qdiffx linear iterations at : 13:59:10 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 3.0855455E-05 4.8217773E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 13:59:11 4.165u 0.218s 0:04.75 92.0% 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 Mon Oct 10 2011 at 13:59:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.841633 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 1.841633 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3122 net assigned charge : 4.000012 assigned positive charge : 488.9228 centred at (gu) : 96.69534 85.10545 91.18349 assigned negative charge : -484.9242 centred at (gu) : 96.69682 85.00989 91.39594 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26364 grid for indexing accessible points = 1.400000 m= 31302 mr = 63033 m= 4244 mr = 23342 m= 180 mr = 2597 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 864 time to turn everything in is 0.7200000 number of dielectric boundary points 35472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24459 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) : 0.6138777 object centre at (A) : 27.98400 3.219000 16.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3017558E-02 -3.8498685E-02 midg,1,midg; midg,igrid,midg 1.0988085E-02 1.2661151E-02 1,midg,midg; igrid,midg,midg 3.3465829E-02 3.5608441E-02 gauss-seidel spectral radius is 0.9985991 estimated iterations to convergence 212 setup time was (sec) 1.040000 now iterating at: 13:59:12 rms-change max change #iterations 4.488762 166.7471 at 10iterations 2.078618 64.61033 at 20iterations 0.9667836 31.37807 at 30iterations 0.4473002 13.71698 at 40iterations 0.2081613 6.157272 at 50iterations 9.6541621E-02 2.784103 at 60iterations 4.4851936E-02 1.472701 at 70iterations 2.0780684E-02 0.6754560 at 80iterations 9.7054718E-03 0.2928162 at 90iterations 4.4952356E-03 0.1375084 at 100iterations 2.0943747E-03 5.8280945E-02 at 110iterations 9.7405928E-04 3.2001495E-02 at 120iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 9.7405928E-04 3.2001495E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 13:59:23 9.542u 0.260s 0:11.94 82.0% 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 Mon Oct 10 2011 at 13:59:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.762450 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 2.762450 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3122 net assigned charge : 4.000012 assigned positive charge : 488.9228 centred at (gu) : 100.0428 82.65800 91.77495 assigned negative charge : -484.9242 centred at (gu) : 100.0451 82.51476 92.09393 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 205551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26364 grid for indexing accessible points = 1.400000 m= 103723 mr = 152803 m= 35264 mr = 85417 m= 7247 mr = 28523 m= 770 mr = 5347 m= 33 mr = 463 m= 0 mr = 7 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2937 time to turn everything in is 1.800000 number of dielectric boundary points 80028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 24969 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) : 1.841633 object centre at (A) : 27.98400 3.219000 16.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3170315 -0.4120190 midg,1,midg; midg,igrid,midg 7.1011469E-02 0.1122128 1,midg,midg; igrid,midg,midg 0.3583556 0.4728788 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 2.160000 now iterating at: 13:59:25 rms-change max change #iterations 10.63048 284.1764 at 10iterations 6.228042 128.2090 at 20iterations 3.621942 66.26831 at 30iterations 2.095630 37.84469 at 40iterations 1.212957 25.54160 at 50iterations 0.7011933 11.66408 at 60iterations 0.4039703 7.155712 at 70iterations 0.2329511 3.778305 at 80iterations 0.1344818 2.411976 at 90iterations 7.7345602E-02 1.405365 at 100iterations 4.4526510E-02 0.7565155 at 110iterations 2.5648331E-02 0.4180508 at 120iterations 1.4790808E-02 0.2452526 at 130iterations 8.5151922E-03 0.1384583 at 140iterations 4.9146512E-03 9.3761444E-02 at 150iterations 2.8397150E-03 4.9616814E-02 at 160iterations 1.6456548E-03 2.8639317E-02 at 170iterations 9.5723663E-04 1.5865564E-02 at 180iterations finished qdiffx linear iterations at : 13:59:39 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 9.5723663E-04 1.5865564E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 13:59:40 15.785u 0.262s 0:16.60 96.6% 0+0k 0+0io 0pf+0w