Wed Dec 28 11:04:25 PST 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 Wed Dec 28 2011 at 11:04:25 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6390579 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 0.6390579 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.31395 92.69924 89.58440 assigned negative charge : -287.4003 centred at (gu) : 90.43836 92.86634 89.50422 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5450 nv = 96 ne = 84 npr = 40260 no. pairs analyzed = 40260 no. exposed pairs = 2478 no. arc points = 17455 no. surface atoms = 849 nbur = 1121 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2975 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2300000 number of dielectric boundary points 2721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7609600E-09 9.1013987E-09 midg,1,midg; midg,igrid,midg 9.5718518E-09 -1.9977792E-08 1,midg,midg; igrid,midg,midg 1.2669116E-08 -7.7130782E-09 gauss-seidel spectral radius is 0.9872591 estimated iterations to convergence 72 setup time was (sec) 0.4500000 now iterating at: 11:04:26 rms-change max change #iterations 0.1189295 21.44173 at 10iterations 1.1755846E-02 1.932983 at 20iterations 1.1365790E-03 0.2018890 at 30iterations 1.1030551E-04 1.7060697E-02 at 40iterations 1.1072269E-05 1.6403198E-03 at 50iterations finished qdiffx linear iterations at : 11:04:28 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.1072269E-05 1.6403198E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 11:04:29 3.086u 0.143s 0:03.54 90.9% 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 Wed Dec 28 2011 at 11:04:29 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.917174 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 1.917174 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.94186 98.09767 88.75291 assigned negative charge : -287.4003 centred at (gu) : 91.31540 98.59934 88.51276 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 58093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17455 grid for indexing accessible points = 1.400000 m= 22268 mr = 39567 m= 3576 mr = 16997 m= 205 mr = 2356 m= 2 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 448 time to turn everything in is 0.5300000 number of dielectric boundary points 25135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14479 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) : 0.6390579 object centre at (A) : 15.36150 22.14850 4.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3042228E-02 8.7867649E-03 midg,1,midg; midg,igrid,midg 3.4402639E-02 -1.6286474E-02 1,midg,midg; igrid,midg,midg 1.1303237E-02 -4.6639796E-03 gauss-seidel spectral radius is 0.9985754 estimated iterations to convergence 210 setup time was (sec) 0.8400000 now iterating at: 11:04:30 rms-change max change #iterations 3.582275 191.7782 at 10iterations 1.647152 70.02506 at 20iterations 0.7585678 28.67114 at 30iterations 0.3492016 12.63778 at 40iterations 0.1611407 5.798231 at 50iterations 7.4320897E-02 2.523845 at 60iterations 3.4126692E-02 1.332787 at 70iterations 1.5670732E-02 0.5382366 at 80iterations 7.2348895E-03 0.3020058 at 90iterations 3.3277685E-03 0.1214294 at 100iterations 1.5323448E-03 5.0917625E-02 at 110iterations 7.0568139E-04 2.1957397E-02 at 120iterations finished qdiffx linear iterations at : 11:04:36 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 7.0568139E-04 2.1957397E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 11:04:37 7.281u 0.323s 0:07.99 95.1% 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 Wed Dec 28 2011 at 11:04:37 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.875761 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): -4.544000 35.26700 ymin,ymax (A): -3.621000 47.91800 zmin,zma (A): -23.58300 32.12400 x,y,z range (A): 39.81100 51.53900 55.70700 scale (grids/A): 2.875761 object centre (A): 15.36150 22.14850 4.270500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 91.41279 102.1465 88.12936 assigned negative charge : -287.4003 centred at (gu) : 91.97311 102.8989 87.76921 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 134056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17455 grid for indexing accessible points = 1.400000 m= 69859 mr = 95705 m= 27208 mr = 57860 m= 6421 mr = 22716 m= 863 mr = 4896 m= 56 mr = 615 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1530 time to turn everything in is 1.060000 number of dielectric boundary points 56638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 14702 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) : 1.917174 object centre at (A) : 15.36150 22.14850 4.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.148121 -1.9240875E-02 midg,1,midg; midg,igrid,midg 0.3878374 -0.2320437 1,midg,midg; igrid,midg,midg 7.8563303E-02 -2.4371551E-02 gauss-seidel spectral radius is 0.9992320 estimated iterations to convergence 285 setup time was (sec) 1.340000 now iterating at: 11:04:38 rms-change max change #iterations 8.468450 500.2089 at 10iterations 4.869240 123.0109 at 20iterations 2.779134 72.52227 at 30iterations 1.591035 37.90025 at 40iterations 0.9066684 25.22884 at 50iterations 0.5160594 12.46061 at 60iterations 0.2944040 6.436872 at 70iterations 0.1673146 3.495373 at 80iterations 9.4859891E-02 1.842247 at 90iterations 5.4004230E-02 1.110655 at 100iterations 3.0615974E-02 0.6231809 at 110iterations 1.7422657E-02 0.3707643 at 120iterations 9.8619834E-03 0.2062950 at 130iterations 5.6093941E-03 0.1186104 at 140iterations 3.1919391E-03 6.4621925E-02 at 150iterations 1.8099197E-03 4.1130066E-02 at 160iterations 1.0275316E-03 1.9748688E-02 at 170iterations 5.8279012E-04 1.0999680E-02 at 180iterations finished qdiffx linear iterations at : 11:04:48 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 5.8279012E-04 1.0999680E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 11:04:49 11.183u 0.229s 0:12.30 92.6% 0+0k 0+0io 0pf+0w