Mon Oct 10 13:55:19 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 Mon Oct 10 2011 at 13:55:19 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 0.6802201 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): -6.959000 44.69700 ymin,ymax (A): -13.85900 38.47700 zmin,zma (A): 2.297000 44.28000 x,y,z range (A): 51.65600 52.33600 41.98300 scale (grids/A): 0.6802201 object centre (A): 18.86900 12.30900 23.28850 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 365.8770 centred at (gu) : 89.68266 90.59491 90.82885 assigned negative charge : -363.3774 centred at (gu) : 89.71662 90.79674 90.88976 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7472 nv = 96 ne = 84 npr = 47847 no. pairs analyzed = 47847 no. exposed pairs = 2998 no. arc points = 21410 no. surface atoms = 1012 nbur = 1373 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4091 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1980 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8578 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5338405E-08 -8.8292698E-09 midg,1,midg; midg,igrid,midg 6.3681775E-08 -5.8509066E-08 1,midg,midg; igrid,midg,midg 2.3218670E-08 9.7447939E-10 gauss-seidel spectral radius is 0.9887758 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 13:55:20 rms-change max change #iterations 0.1848215 25.95988 at 10iterations 2.1383962E-02 2.963358 at 20iterations 3.0329647E-03 0.4742203 at 30iterations 6.9211930E-04 0.1131248 at 40iterations 2.1758539E-04 3.5289764E-02 at 50iterations finished qdiffx linear iterations at : 13:55:23 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.1758539E-04 3.5289764E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:55:23 3.404u 0.181s 0:04.13 86.6% 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 13:55:23 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 2.040660 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): -6.959000 44.69700 ymin,ymax (A): -13.85900 38.47700 zmin,zma (A): 2.297000 44.28000 x,y,z range (A): 51.65600 52.33600 41.98300 scale (grids/A): 2.040660 object centre (A): 18.86900 12.30900 23.28850 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 365.8770 centred at (gu) : 89.04724 91.78435 92.48595 assigned negative charge : -363.3774 centred at (gu) : 89.14976 92.38996 92.66893 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21410 grid for indexing accessible points = 1.400000 m= 30037 mr = 55241 m= 5193 mr = 22165 m= 445 mr = 3243 m= 6 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 690 time to turn everything in is 0.3800000 number of dielectric boundary points 34402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17798 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) : 0.6802201 object centre at (A) : 18.86900 12.30900 23.28850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9120257E-02 5.9262459E-04 midg,1,midg; midg,igrid,midg 1.9373853E-02 -6.4332254E-02 1,midg,midg; igrid,midg,midg 4.7542747E-02 -1.2174120E-02 gauss-seidel spectral radius is 0.9987865 estimated iterations to convergence 227 setup time was (sec) 0.5900000 now iterating at: 13:55:24 rms-change max change #iterations 4.695731 362.6201 at 10iterations 2.290149 77.01297 at 20iterations 1.118193 38.33064 at 30iterations 0.5490909 17.58983 at 40iterations 0.2680039 8.228656 at 50iterations 0.1312429 4.190989 at 60iterations 6.4271450E-02 2.013077 at 70iterations 3.1655308E-02 0.8995838 at 80iterations 1.5660163E-02 0.4485598 at 90iterations 7.8579737E-03 0.2539272 at 100iterations 4.0086228E-03 0.1266441 at 110iterations 2.1470890E-03 7.2406769E-02 at 120iterations finished qdiffx linear iterations at : 13:55:31 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.1470890E-03 7.2406769E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 13:55:32 7.690u 0.222s 0:08.23 96.1% 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 Mon Oct 10 2011 at 13:55:32 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2385 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: 3.060991 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): -6.959000 44.69700 ymin,ymax (A): -13.85900 38.47700 zmin,zma (A): 2.297000 44.28000 x,y,z range (A): 51.65600 52.33600 41.98300 scale (grids/A): 3.060991 object centre (A): 18.86900 12.30900 23.28850 number of atom coordinates read : 2385 total number of charged atoms : 2243 net assigned charge : 2.500020 assigned positive charge : 365.8770 centred at (gu) : 88.57071 92.67631 93.72878 assigned negative charge : -363.3774 centred at (gu) : 88.72463 93.58472 94.00339 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 183740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21410 grid for indexing accessible points = 1.400000 m= 95038 mr = 133388 m= 36221 mr = 77918 m= 9348 mr = 29101 m= 1752 mr = 7025 m= 214 mr = 1274 m= 12 mr = 134 m= 0 mr = 7 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2008 time to turn everything in is 1.030000 number of dielectric boundary points 77478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17944 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) : 2.040660 object centre at (A) : 18.86900 12.30900 23.28850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3938193 -8.9068882E-02 midg,1,midg; midg,igrid,midg 0.4973280 -0.6202768 1,midg,midg; igrid,midg,midg 0.4924549 -0.3934706 gauss-seidel spectral radius is 0.9992894 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 13:55:33 rms-change max change #iterations 10.73303 397.1335 at 10iterations 6.324993 141.7764 at 20iterations 3.735147 76.58067 at 30iterations 2.193218 40.44833 at 40iterations 1.284976 24.08682 at 50iterations 0.7539189 15.15214 at 60iterations 0.4411791 8.945663 at 70iterations 0.2576785 4.824448 at 80iterations 0.1507425 2.600294 at 90iterations 8.7965243E-02 1.562423 at 100iterations 5.1642064E-02 0.9768639 at 110iterations 3.0351944E-02 0.5703812 at 120iterations 1.8074458E-02 0.3435564 at 130iterations 1.0930919E-02 0.2300262 at 140iterations 6.8482272E-03 0.1447754 at 150iterations 4.4906032E-03 9.9803925E-02 at 160iterations 3.1411694E-03 7.0190430E-02 at 170iterations 2.3312259E-03 5.4374695E-02 at 180iterations finished qdiffx linear iterations at : 13:55:45 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 2.3312259E-03 5.4374695E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 13:55:46 13.373u 0.274s 0:13.98 97.5% 0+0k 0+0io 0pf+0w