Mon Oct 10 14:04:29 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 14:04:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7295979 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): 43.19200 91.98600 ymin,ymax (A): 50.54800 96.53800 zmin,zma (A): 5.141000 53.00400 x,y,z range (A): 48.79400 45.99000 47.86300 scale (grids/A): 0.7295979 object centre (A): 67.58900 73.54300 29.07250 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 90.15707 89.43685 90.05311 assigned negative charge : -324.1440 centred at (gu) : 90.26768 89.41611 89.84765 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7721 nv = 96 ne = 84 npr = 44067 no. pairs analyzed = 44067 no. exposed pairs = 2638 no. arc points = 18639 no. surface atoms = 895 nbur = 1233 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 567 mr = 4357 m= 3 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.1700000 number of dielectric boundary points 3795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1592 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8386 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4118941E-07 9.8473095E-08 midg,1,midg; midg,igrid,midg -9.6530712E-08 -4.7521866E-08 1,midg,midg; igrid,midg,midg 2.0334298E-08 -1.6739838E-07 gauss-seidel spectral radius is 0.9902134 estimated iterations to convergence 82 setup time was (sec) 0.3600000 now iterating at: 14:04:30 rms-change max change #iterations 0.2316654 29.59347 at 10iterations 3.0559052E-02 3.836906 at 20iterations 3.9545787E-03 0.6248436 at 30iterations 5.2298198E-04 6.2339783E-02 at 40iterations 6.8153997E-05 9.1533661E-03 at 50iterations finished qdiffx linear iterations at : 14:04:32 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.8153997E-05 9.1533661E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:04:33 3.305u 0.171s 0:04.09 84.8% 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 14:04:33 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 = 2128 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: 2.188794 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): 43.19200 91.98600 ymin,ymax (A): 50.54800 96.53800 zmin,zma (A): 5.141000 53.00400 x,y,z range (A): 48.79400 45.99000 47.86300 scale (grids/A): 2.188794 object centre (A): 67.58900 73.54300 29.07250 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 90.47117 88.31042 90.15919 assigned negative charge : -324.1440 centred at (gu) : 90.80283 88.24825 89.54300 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18639 grid for indexing accessible points = 1.400000 m= 32193 mr = 56238 m= 6820 mr = 24713 m= 716 mr = 4812 m= 17 mr = 442 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2421 time to turn everything in is 0.4000000 number of dielectric boundary points 34846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15818 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) : 0.7295979 object centre at (A) : 67.58900 73.54300 29.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1315709 1.2919385E-02 midg,1,midg; midg,igrid,midg -3.1958997E-02 -2.2517467E-02 1,midg,midg; igrid,midg,midg 5.9243510E-03 -3.3176586E-02 gauss-seidel spectral radius is 0.9989009 estimated iterations to convergence 239 setup time was (sec) 0.6200000 now iterating at: 14:04:34 rms-change max change #iterations 4.986437 207.7808 at 10iterations 2.511665 77.49268 at 20iterations 1.270052 37.25860 at 30iterations 0.6427081 18.32440 at 40iterations 0.3244448 11.48162 at 50iterations 0.1642953 5.040587 at 60iterations 8.3292462E-02 2.285248 at 70iterations 4.2078305E-02 1.341141 at 80iterations 2.1283234E-02 0.5996161 at 90iterations 1.0765114E-02 0.3144715 at 100iterations 5.4420996E-03 0.1571751 at 110iterations 2.7608399E-03 8.3055496E-02 at 120iterations finished qdiffx linear iterations at : 14:04:41 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.7608399E-03 8.3055496E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:04:42 7.732u 0.189s 0:08.67 91.2% 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 14:04:42 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 = 2128 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: 3.283190 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): 43.19200 91.98600 ymin,ymax (A): 50.54800 96.53800 zmin,zma (A): 5.141000 53.00400 x,y,z range (A): 48.79400 45.99000 47.86300 scale (grids/A): 3.283190 object centre (A): 67.58900 73.54300 29.07250 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 90.70680 87.46557 90.23887 assigned negative charge : -324.1440 centred at (gu) : 91.20438 87.37239 89.31464 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 187224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18639 grid for indexing accessible points = 1.400000 m= 98913 mr = 135301 m= 41923 mr = 82333 m= 13109 mr = 34961 m= 3064 mr = 10533 m= 391 mr = 2502 m= 23 mr = 274 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 8141 time to turn everything in is 1.240000 number of dielectric boundary points 78731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 15908 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) : 2.188794 object centre at (A) : 67.58900 73.54300 29.07250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.285116 0.2195542 midg,1,midg; midg,igrid,midg -0.2354176 -0.2161764 1,midg,midg; igrid,midg,midg -7.6577157E-02 -0.2792585 gauss-seidel spectral radius is 0.9993137 estimated iterations to convergence 301 setup time was (sec) 1.470000 now iterating at: 14:04:44 rms-change max change #iterations 10.85227 332.5156 at 10iterations 6.378617 124.2222 at 20iterations 3.747639 68.34721 at 30iterations 2.200917 41.98267 at 40iterations 1.292727 21.35623 at 50iterations 0.7587377 12.65140 at 60iterations 0.4458835 7.334259 at 70iterations 0.2609484 4.421893 at 80iterations 0.1530772 2.496368 at 90iterations 8.9719795E-02 1.465594 at 100iterations 5.2499585E-02 0.8958507 at 110iterations 3.0704508E-02 0.4816966 at 120iterations 1.8050792E-02 0.2973739 at 130iterations 1.0565017E-02 0.1706810 at 140iterations 6.1915689E-03 9.7343445E-02 at 150iterations 3.6256872E-03 5.8475494E-02 at 160iterations 2.1265375E-03 3.2234192E-02 at 170iterations 1.2491018E-03 2.0966530E-02 at 180iterations finished qdiffx linear iterations at : 14:04:55 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 1.2491018E-03 2.0966530E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 14:04:55 12.797u 0.211s 0:13.58 95.7% 0+0k 0+0io 0pf+0w