Sat Oct 8 18:29:43 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 Sat Oct 8 2011 at 18:29:43 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 508 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6243971 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): -32.07300 17.59100 ymin,ymax (A): -23.85000 23.19000 zmin,zma (A): -12.27900 44.73600 x,y,z range (A): 49.66400 47.04000 57.01500 scale (grids/A): 0.6243971 object centre (A): -7.240999 -0.3299999 16.22850 number of atom coordinates read : 2551 total number of charged atoms : 2464 net assigned charge : 5.000006 assigned positive charge : 392.7960 centred at (gu) : 88.59291 89.25494 89.78255 assigned negative charge : -387.7966 centred at (gu) : 88.48352 89.29831 89.68043 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 51342 no. pairs analyzed = 51342 no. exposed pairs = 3070 no. arc points = 21754 no. surface atoms = 1031 nbur = 1520 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3695 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2181 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8173 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2105467E-09 1.1739257E-08 midg,1,midg; midg,igrid,midg 9.3646779E-09 1.2569730E-09 1,midg,midg; igrid,midg,midg -5.0581654E-09 9.4647463E-09 gauss-seidel spectral radius is 0.9867111 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 18:29:43 rms-change max change #iterations 0.1296394 19.86668 at 10iterations 1.2358378E-02 1.883652 at 20iterations 1.1465068E-03 0.1908588 at 30iterations 1.1152284E-04 2.0519257E-02 at 40iterations 1.0697393E-05 1.3580322E-03 at 50iterations finished qdiffx linear iterations at : 18:29:46 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.0697393E-05 1.3580322E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 18:29:47 3.697u 0.215s 0:04.24 91.9% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 18:29:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 508 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.873191 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): -32.07300 17.59100 ymin,ymax (A): -23.85000 23.19000 zmin,zma (A): -12.27900 44.73600 x,y,z range (A): 49.66400 47.04000 57.01500 scale (grids/A): 1.873191 object centre (A): -7.240999 -0.3299999 16.22850 number of atom coordinates read : 2551 total number of charged atoms : 2464 net assigned charge : 5.000006 assigned positive charge : 392.7960 centred at (gu) : 85.77838 87.76413 89.34714 assigned negative charge : -387.7966 centred at (gu) : 85.45029 87.89473 89.04105 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21754 grid for indexing accessible points = 1.400000 m= 26280 mr = 50619 m= 3918 mr = 19601 m= 212 mr = 2429 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1578 time to turn everything in is 0.3700000 number of dielectric boundary points 30007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19373 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) : 0.6243971 object centre at (A) : -7.240999 -0.3299999 16.22850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8157702E-02 2.9544398E-02 midg,1,midg; midg,igrid,midg 1.4815507E-02 3.5682940E-03 1,midg,midg; igrid,midg,midg -1.2277189E-03 3.8366493E-02 gauss-seidel spectral radius is 0.9985874 estimated iterations to convergence 211 setup time was (sec) 0.6200000 now iterating at: 18:29:48 rms-change max change #iterations 4.067623 159.1313 at 10iterations 1.880344 67.81310 at 20iterations 0.8711717 31.12702 at 30iterations 0.4027618 13.86205 at 40iterations 0.1875636 7.423630 at 50iterations 8.6545236E-02 2.595061 at 60iterations 4.0119052E-02 1.185440 at 70iterations 1.8603859E-02 0.5620308 at 80iterations 8.5409572E-03 0.2842407 at 90iterations 3.9792932E-03 0.1409118 at 100iterations 1.8371348E-03 5.3937912E-02 at 110iterations 8.4967841E-04 2.7636528E-02 at 120iterations finished qdiffx linear iterations at : 18:29:56 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 8.4967841E-04 2.7636528E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 18:29:56 8.664u 0.271s 0:09.25 96.5% 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 Sat Oct 8 2011 at 18:29:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 508 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.809787 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): -32.07300 17.59100 ymin,ymax (A): -23.85000 23.19000 zmin,zma (A): -12.27900 44.73600 x,y,z range (A): 49.66400 47.04000 57.01500 scale (grids/A): 2.809787 object centre (A): -7.240999 -0.3299999 16.22850 number of atom coordinates read : 2551 total number of charged atoms : 2464 net assigned charge : 5.000006 assigned positive charge : 392.7960 centred at (gu) : 83.66744 86.64608 89.02064 assigned negative charge : -387.7966 centred at (gu) : 83.17551 86.84207 88.56158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21754 grid for indexing accessible points = 1.400000 m= 85674 mr = 121976 m= 30380 mr = 70897 m= 6917 mr = 24475 m= 914 mr = 5150 m= 44 mr = 617 m= 0 mr = 12 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4904 time to turn everything in is 0.9300000 number of dielectric boundary points 67715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19711 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) : 1.873191 object centre at (A) : -7.240999 -0.3299999 16.22850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1369483 0.3922048 midg,1,midg; midg,igrid,midg 0.1723321 2.8981181E-02 1,midg,midg; igrid,midg,midg 1.5398016E-02 0.4733164 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 18:29:58 rms-change max change #iterations 9.556434 403.1580 at 10iterations 5.527306 116.7176 at 20iterations 3.174336 66.01250 at 30iterations 1.820902 34.91661 at 40iterations 1.043539 20.53664 at 50iterations 0.5959872 11.34147 at 60iterations 0.3413661 7.626160 at 70iterations 0.1954263 4.339100 at 80iterations 0.1114182 1.998791 at 90iterations 6.3739032E-02 1.214976 at 100iterations 3.6317427E-02 0.6825747 at 110iterations 2.0745438E-02 0.3933754 at 120iterations 1.1843532E-02 0.2201099 at 130iterations 6.7681996E-03 0.1325188 at 140iterations 3.8690381E-03 7.3715210E-02 at 150iterations 2.2138734E-03 4.4303894E-02 at 160iterations 1.2713623E-03 2.2130966E-02 at 170iterations 7.3165930E-04 1.3489723E-02 at 180iterations finished qdiffx linear iterations at : 18:30:10 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 7.3165930E-04 1.3489723E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 18:30:11 13.785u 0.285s 0:14.34 98.0% 0+0k 0+0io 0pf+0w