Wed Dec 28 11:02:02 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+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 Wed Dec 28 2011 at 11:02:03 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 0.6426457 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 0.6426457 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 290.6140 centred at (gu) : 90.07777 92.89236 90.02258 assigned negative charge : -285.9333 centred at (gu) : 90.13816 92.99213 89.95358 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5665 nv = 96 ne = 84 npr = 40237 no. pairs analyzed = 40237 no. exposed pairs = 2356 no. arc points = 16989 no. surface atoms = 800 nbur = 1163 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 3244 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 2678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2345696E-09 1.3917267E-08 midg,1,midg; midg,igrid,midg 9.0891703E-09 -3.5722676E-09 1,midg,midg; igrid,midg,midg 1.2862957E-08 2.0644235E-09 gauss-seidel spectral radius is 0.9873990 estimated iterations to convergence 73 setup time was (sec) 0.6300000 now iterating at: 11:02:04 rms-change max change #iterations 0.1255504 17.86572 at 10iterations 1.2533416E-02 1.926369 at 20iterations 1.2869951E-03 0.2350731 at 30iterations 1.2549943E-04 2.2026062E-02 at 40iterations 1.2578566E-05 1.6517639E-03 at 50iterations finished qdiffx linear iterations at : 11:02:08 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 1.2578566E-05 1.6517639E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 11:02:09 4.753u 0.453s 0:06.80 76.4% 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 11:02:09 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 1.927937 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 1.927937 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 290.6140 centred at (gu) : 90.23328 98.67696 90.06755 assigned negative charge : -285.9333 centred at (gu) : 90.41485 98.97666 89.86092 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16989 grid for indexing accessible points = 1.400000 m= 23145 mr = 41908 m= 3589 mr = 18066 m= 156 mr = 2345 m= 8 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1830 time to turn everything in is 0.5700000 number of dielectric boundary points 24588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14412 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) : 0.6426457 object centre at (A) : 15.74700 22.07950 3.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9502093E-02 2.4891898E-02 midg,1,midg; midg,igrid,midg 3.5462484E-02 3.9351010E-03 1,midg,midg; igrid,midg,midg 6.0637025E-03 -4.0447721E-04 gauss-seidel spectral radius is 0.9985886 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 11:02:11 rms-change max change #iterations 3.666137 172.5987 at 10iterations 1.699299 66.50571 at 20iterations 0.7881588 27.89133 at 30iterations 0.3647569 14.58707 at 40iterations 0.1679524 5.695275 at 50iterations 7.7506617E-02 2.656618 at 60iterations 3.5888284E-02 1.362829 at 70iterations 1.6635347E-02 0.5659628 at 80iterations 7.6638153E-03 0.2577362 at 90iterations 3.5575517E-03 0.1176715 at 100iterations 1.6427751E-03 6.1325550E-02 at 110iterations 7.5966201E-04 2.6141703E-02 at 120iterations finished qdiffx linear iterations at : 11:02:21 total time elapsed so far: 10.93000 # loops : 120 mean,max change (kT/e) : 7.5966201E-04 2.6141703E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 11:02:22 11.120u 0.544s 0:12.22 95.4% 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 11:02:22 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 2.891906 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): -3.732000 35.22600 ymin,ymax (A): -4.584000 48.74300 zmin,zma (A): -24.06200 31.33400 x,y,z range (A): 38.95800 53.32700 55.39600 scale (grids/A): 2.891906 object centre (A): 15.74700 22.07950 3.636000 number of atom coordinates read : 1963 total number of charged atoms : 1830 net assigned charge : 4.681007 assigned positive charge : 290.6140 centred at (gu) : 90.34994 103.0155 90.10143 assigned negative charge : -285.9333 centred at (gu) : 90.62228 103.4650 89.79140 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 138685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16989 grid for indexing accessible points = 1.400000 m= 73160 mr = 101066 m= 28118 mr = 61409 m= 6340 mr = 23702 m= 792 mr = 4934 m= 49 mr = 565 m= 0 mr = 20 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 6284 time to turn everything in is 1.440000 number of dielectric boundary points 55448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 14637 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) : 1.927937 object centre at (A) : 15.74700 22.07950 3.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.112643 9.8980613E-02 midg,1,midg; midg,igrid,midg 0.3485943 2.4711362E-03 1,midg,midg; igrid,midg,midg 3.6631893E-02 2.6512798E-03 gauss-seidel spectral radius is 0.9992330 estimated iterations to convergence 285 setup time was (sec) 1.850000 now iterating at: 11:02:24 rms-change max change #iterations 8.532391 378.3978 at 10iterations 4.885398 111.9408 at 20iterations 2.776507 64.18404 at 30iterations 1.570290 35.48266 at 40iterations 0.8937838 19.02138 at 50iterations 0.5075350 10.27906 at 60iterations 0.2880199 6.227264 at 70iterations 0.1632427 3.439529 at 80iterations 9.2726953E-02 1.787617 at 90iterations 5.2576456E-02 1.104329 at 100iterations 2.9815070E-02 0.6286700 at 110iterations 1.6891832E-02 0.3417549 at 120iterations 9.5727528E-03 0.1915131 at 130iterations 5.4385350E-03 0.1041816 at 140iterations 3.0873909E-03 6.4033508E-02 at 150iterations 1.7537485E-03 3.5696983E-02 at 160iterations 9.9395111E-04 1.8218994E-02 at 170iterations 5.6643755E-04 1.1749268E-02 at 180iterations finished qdiffx linear iterations at : 11:02:42 total time elapsed so far: 19.92000 # loops : 180 mean,max change (kT/e) : 5.6643755E-04 1.1749268E-02 energy calculations done at 19.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.11000 DelPhi exited at 11:02:43 20.106u 0.587s 0:21.63 95.6% 0+0k 0+0io 0pf+0w