Sat Oct 15 13:00:31 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 15 2011 at 13:00:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6125996 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 0.6125996 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2645 net assigned charge : 4.000008 assigned positive charge : 421.7183 centred at (gu) : 89.37900 89.13274 89.88818 assigned negative charge : -417.7194 centred at (gu) : 89.32909 89.24403 89.73898 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6863 nv = 96 ne = 84 npr = 56133 no. pairs analyzed = 56133 no. exposed pairs = 3610 no. arc points = 24865 no. surface atoms = 1209 nbur = 1576 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3566 m= 0 mr = 30 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3300000 number of dielectric boundary points 3595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2538 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8540 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3547874E-09 1.0708423E-08 midg,1,midg; midg,igrid,midg 1.0770054E-08 -3.2218042E-09 1,midg,midg; igrid,midg,midg -4.2290291E-10 4.7040869E-09 gauss-seidel spectral radius is 0.9862202 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 13:00:32 rms-change max change #iterations 0.1203825 20.21962 at 10iterations 1.0845016E-02 1.698811 at 20iterations 9.7889756E-04 0.1436481 at 30iterations 9.7805452E-05 1.4839172E-02 at 40iterations 1.6418930E-05 3.2482147E-03 at 50iterations finished qdiffx linear iterations at : 13:00:34 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.6418930E-05 3.2482147E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 13:00:35 3.469u 0.154s 0:03.93 91.8% 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 Sat Oct 15 2011 at 13:00:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.837799 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 1.837799 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2645 net assigned charge : 4.000008 assigned positive charge : 421.7183 centred at (gu) : 88.13623 87.39748 89.66377 assigned negative charge : -417.7194 centred at (gu) : 87.98706 87.73188 89.21661 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24865 grid for indexing accessible points = 1.400000 m= 25179 mr = 50786 m= 3501 mr = 17616 m= 210 mr = 1936 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 33150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20697 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) : 0.6125996 object centre at (A) : 15.15750 0.3915005 44.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4345452E-03 1.6822379E-02 midg,1,midg; midg,igrid,midg 2.5237033E-02 6.4630690E-03 1,midg,midg; igrid,midg,midg -4.2539902E-02 -3.8539681E-03 gauss-seidel spectral radius is 0.9985621 estimated iterations to convergence 209 setup time was (sec) 0.8600000 now iterating at: 13:00:36 rms-change max change #iterations 4.148393 179.5478 at 10iterations 1.901935 75.00478 at 20iterations 0.8714622 34.62427 at 30iterations 0.4003045 13.39299 at 40iterations 0.1827893 5.899290 at 50iterations 8.4078573E-02 2.733278 at 60iterations 3.8469777E-02 1.282112 at 70iterations 1.7691040E-02 0.6043358 at 80iterations 8.0927424E-03 0.2788410 at 90iterations 3.7211010E-03 0.1289654 at 100iterations 1.7078519E-03 5.1649570E-02 at 110iterations 7.8738300E-04 2.5821686E-02 at 120iterations finished qdiffx linear iterations at : 13:00:43 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 7.8738300E-04 2.5821686E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 13:00:43 7.674u 0.171s 0:08.12 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 15 2011 at 13:00:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.756698 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): -13.89900 44.21400 ymin,ymax (A): -24.67200 25.45500 zmin,zma (A): 21.54600 68.30400 x,y,z range (A): 58.11300 50.12700 46.75800 scale (grids/A): 2.756698 object centre (A): 15.15750 0.3915005 44.92500 number of atom coordinates read : 2785 total number of charged atoms : 2645 net assigned charge : 4.000008 assigned positive charge : 421.7183 centred at (gu) : 87.20429 86.09599 89.49544 assigned negative charge : -417.7194 centred at (gu) : 86.98050 86.59767 88.82498 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 172908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24865 grid for indexing accessible points = 1.400000 m= 83741 mr = 123830 m= 27765 mr = 66673 m= 5880 mr = 21283 m= 768 mr = 4068 m= 39 mr = 478 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 74757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 21151 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) : 1.837799 object centre at (A) : 15.15750 0.3915005 44.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5793083E-02 0.1024828 midg,1,midg; midg,igrid,midg 0.2496687 8.5522689E-02 1,midg,midg; igrid,midg,midg -0.6811492 1.4315072E-02 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.690000 now iterating at: 13:00:45 rms-change max change #iterations 9.994287 315.9644 at 10iterations 5.918402 150.2763 at 20iterations 3.457601 76.39560 at 30iterations 2.013465 47.24003 at 40iterations 1.166294 25.00072 at 50iterations 0.6758049 13.29215 at 60iterations 0.3896121 7.899114 at 70iterations 0.2240920 4.287621 at 80iterations 0.1287419 2.435122 at 90iterations 7.4050359E-02 1.480278 at 100iterations 4.2423200E-02 0.8398094 at 110iterations 2.4291549E-02 0.4385090 at 120iterations 1.3929269E-02 0.2684135 at 130iterations 7.9702921E-03 0.1362305 at 140iterations 4.5740446E-03 8.8413239E-02 at 150iterations 2.6103233E-03 4.8633575E-02 at 160iterations 1.4954519E-03 2.5741577E-02 at 170iterations 8.5558399E-04 1.7353058E-02 at 180iterations finished qdiffx linear iterations at : 13:00:56 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 8.5558399E-04 1.7353058E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 13:00:57 12.954u 0.190s 0:13.48 97.4% 0+0k 0+0io 0pf+0w