Sun Oct 9 11:31:45 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 Sun Oct 9 2011 at 11:31:45 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 0.5820703 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 0.5820703 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.252016 assigned positive charge : 451.6977 centred at (gu) : 89.54458 90.99487 91.06428 assigned negative charge : -446.4476 centred at (gu) : 89.55918 90.96592 91.01418 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 59240 no. pairs analyzed = 59240 no. exposed pairs = 4087 no. arc points = 28924 no. surface atoms = 1357 nbur = 1677 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 346 mr = 3539 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3100000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2884 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4378314E-11 3.0546179E-09 midg,1,midg; midg,igrid,midg 4.2277332E-10 2.3773219E-09 1,midg,midg; igrid,midg,midg 1.7217049E-09 7.7890056E-10 gauss-seidel spectral radius is 0.9847810 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 11:31:46 rms-change max change #iterations 9.8836876E-02 14.00249 at 10iterations 7.9913111E-03 1.107721 at 20iterations 8.1869029E-04 0.1215439 at 30iterations 1.3799735E-04 2.2010803E-02 at 40iterations 3.0998686E-05 4.8713684E-03 at 50iterations finished qdiffx linear iterations at : 11:31:48 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.0998686E-05 4.8713684E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 11:31:49 3.113u 0.164s 0:03.54 92.3% 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 Sun Oct 9 2011 at 11:31:49 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 1.746211 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 1.746211 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.252016 assigned positive charge : 451.6977 centred at (gu) : 88.63243 92.98379 93.19183 assigned negative charge : -446.4476 centred at (gu) : 88.67759 92.89756 93.04234 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28924 grid for indexing accessible points = 1.400000 m= 25422 mr = 51328 m= 3398 mr = 17465 m= 133 mr = 1788 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.5200000 number of dielectric boundary points 34928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22713 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) : 0.5820703 object centre at (A) : -19.90250 -1.9499779E-02 -0.4939995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3766862E-03 1.0448703E-02 midg,1,midg; midg,igrid,midg 1.1209982E-02 1.9214628E-02 1,midg,midg; igrid,midg,midg 1.6349947E-02 -3.6990175E-03 gauss-seidel spectral radius is 0.9984478 estimated iterations to convergence 201 setup time was (sec) 0.7800000 now iterating at: 11:31:49 rms-change max change #iterations 3.868682 159.1943 at 10iterations 1.706551 54.12804 at 20iterations 0.7595800 24.42445 at 30iterations 0.3387469 10.65861 at 40iterations 0.1506626 4.706215 at 50iterations 6.6888265E-02 2.243530 at 60iterations 2.9801650E-02 0.9036732 at 70iterations 1.3352245E-02 0.4271111 at 80iterations 5.9360410E-03 0.1866503 at 90iterations 2.6706022E-03 8.6253166E-02 at 100iterations 1.2048327E-03 4.0741324E-02 at 110iterations 5.4573861E-04 1.9321442E-02 at 120iterations finished qdiffx linear iterations at : 11:31:56 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 5.4573861E-04 1.9321442E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 11:31:56 7.031u 0.170s 0:07.50 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 Sun Oct 9 2011 at 11:31:56 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: CME 459 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of 0.1000 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: 2.619316 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): -50.48300 10.67800 ymin,ymax (A): -25.15800 25.11900 zmin,zma (A): -28.81000 27.82200 x,y,z range (A): 61.16100 50.27700 56.63200 scale (grids/A): 2.619316 object centre (A): -19.90250 -1.9499779E-02 -0.4939995 number of atom coordinates read : 3034 total number of charged atoms : 2921 net assigned charge : 5.252016 assigned positive charge : 451.6977 centred at (gu) : 87.94843 94.47560 94.78764 assigned negative charge : -446.4476 centred at (gu) : 88.01653 94.34640 94.56342 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 177635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28924 grid for indexing accessible points = 1.400000 m= 83964 mr = 125898 m= 27451 mr = 65760 m= 5783 mr = 20751 m= 584 mr = 3940 m= 16 mr = 316 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1682 time to turn everything in is 1.270000 number of dielectric boundary points 78768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 23364 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) : 1.746211 object centre at (A) : -19.90250 -1.9499779E-02 -0.4939995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7549140E-02 0.1208871 midg,1,midg; midg,igrid,midg 0.2097534 0.2790593 1,midg,midg; igrid,midg,midg 0.2959501 -9.1026001E-02 gauss-seidel spectral radius is 0.9992244 estimated iterations to convergence 283 setup time was (sec) 1.550000 now iterating at: 11:31:58 rms-change max change #iterations 9.583506 262.6869 at 10iterations 5.595054 173.8597 at 20iterations 3.228874 77.52206 at 30iterations 1.862435 40.49332 at 40iterations 1.068004 23.49374 at 50iterations 0.6112500 14.17696 at 60iterations 0.3487739 6.510735 at 70iterations 0.1988363 4.428455 at 80iterations 0.1130132 2.199480 at 90iterations 6.4524502E-02 1.254274 at 100iterations 3.6610242E-02 0.7219810 at 110iterations 2.0808861E-02 0.3994684 at 120iterations 1.1830555E-02 0.2176032 at 130iterations 6.7229988E-03 0.1302719 at 140iterations 3.8307635E-03 6.8016052E-02 at 150iterations 2.1815074E-03 4.1854858E-02 at 160iterations 1.2466598E-03 2.4402618E-02 at 170iterations 7.1682065E-04 1.3277054E-02 at 180iterations finished qdiffx linear iterations at : 11:32:08 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 7.1682065E-04 1.3277054E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 11:32:08 11.544u 0.197s 0:12.06 97.2% 0+0k 0+0io 0pf+0w