Tue Oct 11 08:20:05 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+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 Tue Oct 11 2011 at 08:20:05 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7384207 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 0.7384207 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 176.1781 centred at (gu) : 88.71839 89.08040 88.69524 assigned negative charge : -170.6781 centred at (gu) : 88.41425 89.06785 88.70727 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4385 nv = 96 ne = 84 npr = 21960 no. pairs analyzed = 21960 no. exposed pairs = 1505 no. arc points = 11149 no. surface atoms = 502 nbur = 645 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2271 m= 0 mr = 51 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 979 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2964433E-07 7.0951415E-08 midg,1,midg; midg,igrid,midg 1.0544930E-07 8.6734211E-08 1,midg,midg; igrid,midg,midg -8.8685205E-08 1.9697769E-07 gauss-seidel spectral radius is 0.9903479 estimated iterations to convergence 83 setup time was (sec) 0.3000000 now iterating at: 08:20:05 rms-change max change #iterations 0.1738177 29.13630 at 10iterations 2.3021264E-02 4.901035 at 20iterations 3.0104353E-03 0.5451450 at 30iterations 3.9842704E-04 6.9458008E-02 at 40iterations 5.2976149E-05 8.6145401E-03 at 50iterations finished qdiffx linear iterations at : 08:20:08 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 5.2976149E-05 8.6145401E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 08:20:09 3.304u 0.163s 0:03.97 87.1% 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 Tue Oct 11 2011 at 08:20:09 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.215262 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 2.215262 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 176.1781 centred at (gu) : 86.15530 87.24123 86.08578 assigned negative charge : -170.6781 centred at (gu) : 85.24287 87.20376 86.12196 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11149 grid for indexing accessible points = 1.400000 m= 17609 mr = 29356 m= 3628 mr = 13138 m= 370 mr = 2535 m= 22 mr = 224 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 21704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8436 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) : 0.7384207 object centre at (A) : 12.98200 20.96200 22.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6050776E-02 3.9779255E-03 midg,1,midg; midg,igrid,midg 3.8062841E-02 3.1513397E-02 1,midg,midg; igrid,midg,midg -2.8734773E-02 4.0063344E-02 gauss-seidel spectral radius is 0.9988303 estimated iterations to convergence 231 setup time was (sec) 0.4700000 now iterating at: 08:20:10 rms-change max change #iterations 3.600472 231.3290 at 10iterations 1.783038 80.11943 at 20iterations 0.8773430 35.84494 at 30iterations 0.4383406 17.77189 at 40iterations 0.2142737 8.150532 at 50iterations 0.1059222 4.298345 at 60iterations 5.2186318E-02 1.961335 at 70iterations 2.5750075E-02 1.017329 at 80iterations 1.2741085E-02 0.4634056 at 90iterations 6.3231271E-03 0.2262192 at 100iterations 3.1222303E-03 0.1264515 at 110iterations 1.5398852E-03 6.2782288E-02 at 120iterations finished qdiffx linear iterations at : 08:20:17 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.5398852E-03 6.2782288E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 08:20:17 7.571u 0.187s 0:08.07 96.0% 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 Tue Oct 11 2011 at 08:20:17 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.322893 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 3.322893 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 176.1781 centred at (gu) : 84.23307 85.86188 84.12872 assigned negative charge : -170.6781 centred at (gu) : 82.86436 85.80569 84.18304 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 104261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11149 grid for indexing accessible points = 1.400000 m= 53627 mr = 71002 m= 22736 mr = 43683 m= 6920 mr = 18718 m= 1483 mr = 5567 m= 220 mr = 1146 m= 25 mr = 172 m= 0 mr = 23 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 48961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 8464 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) : 2.215262 object centre at (A) : 12.98200 20.96200 22.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3212607 2.1362741E-02 midg,1,midg; midg,igrid,midg 0.3411371 0.2827185 1,midg,midg; igrid,midg,midg -0.2242230 0.2973123 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 0.9500000 now iterating at: 08:20:18 rms-change max change #iterations 7.932760 376.7645 at 10iterations 4.621981 132.5932 at 20iterations 2.684541 64.09080 at 30iterations 1.549852 39.01844 at 40iterations 0.9005190 19.54709 at 50iterations 0.5223517 11.02618 at 60iterations 0.3031942 6.797860 at 70iterations 0.1762048 3.823151 at 80iterations 0.1019963 2.150152 at 90iterations 5.8936518E-02 1.260176 at 100iterations 3.4224939E-02 0.7098584 at 110iterations 1.9809969E-02 0.4259098 at 120iterations 1.1503673E-02 0.2447248 at 130iterations 6.6771279E-03 0.1594372 at 140iterations 3.8813590E-03 8.1124961E-02 at 150iterations 2.2534956E-03 4.6029091E-02 at 160iterations 1.3054847E-03 2.6843071E-02 at 170iterations 7.5714703E-04 1.6010284E-02 at 180iterations finished qdiffx linear iterations at : 08:20:29 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 7.5714703E-04 1.6010284E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 08:20:30 11.931u 0.220s 0:12.65 96.0% 0+0k 0+0io 0pf+0w