Tue Oct 11 00:55:41 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 00:55:42 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 0.6196045 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 0.6196045 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2554 net assigned charge : 6.040018 assigned positive charge : 407.6728 centred at (gu) : 90.61725 90.20486 90.13632 assigned negative charge : -401.6333 centred at (gu) : 90.41151 90.37675 90.31173 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6884 nv = 96 ne = 84 npr = 53207 no. pairs analyzed = 53207 no. exposed pairs = 3223 no. arc points = 22674 no. surface atoms = 1080 nbur = 1593 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3934 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.4000000 number of dielectric boundary points 3271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6002314E-08 -7.6176647E-09 midg,1,midg; midg,igrid,midg 1.5542735E-08 -7.4805140E-09 1,midg,midg; igrid,midg,midg -8.2702600E-09 2.1185194E-08 gauss-seidel spectral radius is 0.9865152 estimated iterations to convergence 70 setup time was (sec) 0.6900000 now iterating at: 00:55:43 rms-change max change #iterations 0.1307084 19.01050 at 10iterations 1.2443642E-02 1.824841 at 20iterations 1.5975218E-03 0.3086090 at 30iterations 3.9551448E-04 9.1270447E-02 at 40iterations 1.1863474E-04 2.8671265E-02 at 50iterations finished qdiffx linear iterations at : 00:55:46 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.1863474E-04 2.8671265E-02 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 00:55:47 4.155u 0.180s 0:05.14 84.2% 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 00:55:47 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 1.858814 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 1.858814 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2554 net assigned charge : 6.040018 assigned positive charge : 407.6728 centred at (gu) : 91.85165 90.61413 90.40839 assigned negative charge : -401.6333 centred at (gu) : 91.23409 91.12998 90.93493 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22674 grid for indexing accessible points = 1.400000 m= 27271 mr = 53137 m= 4122 mr = 20527 m= 193 mr = 2632 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2551 time to turn everything in is 0.7200000 number of dielectric boundary points 30315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20028 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) : 0.6196045 object centre at (A) : 51.21950 30.74100 48.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9663157E-02 7.1046837E-03 midg,1,midg; midg,igrid,midg 2.6302187E-02 -6.1506346E-02 1,midg,midg; igrid,midg,midg -1.5526820E-02 7.8890331E-02 gauss-seidel spectral radius is 0.9985734 estimated iterations to convergence 210 setup time was (sec) 1.070000 now iterating at: 00:55:48 rms-change max change #iterations 4.149246 182.6358 at 10iterations 1.895185 70.49886 at 20iterations 0.8724344 29.46077 at 30iterations 0.4034892 12.77057 at 40iterations 0.1853597 6.106552 at 50iterations 8.5712239E-02 2.853546 at 60iterations 3.9591536E-02 1.350546 at 70iterations 1.8320138E-02 0.6485844 at 80iterations 8.5901925E-03 0.2785139 at 90iterations 4.0644594E-03 0.1312675 at 100iterations 1.9909577E-03 7.3291779E-02 at 110iterations 1.0292367E-03 3.9409637E-02 at 120iterations finished qdiffx linear iterations at : 00:55:56 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 1.0292367E-03 3.9409637E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 00:55:57 9.350u 0.221s 0:10.10 94.7% 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 00:55:57 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 2.788220 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): 23.09900 79.34000 ymin,ymax (A): 2.013000 59.46900 zmin,zma (A): 27.18700 69.30900 x,y,z range (A): 56.24100 57.45600 42.12200 scale (grids/A): 2.788220 object centre (A): 51.21950 30.74100 48.24800 number of atom coordinates read : 2673 total number of charged atoms : 2554 net assigned charge : 6.040018 assigned positive charge : 407.6728 centred at (gu) : 92.77730 90.92122 90.61240 assigned negative charge : -401.6333 centred at (gu) : 91.85091 91.69494 91.40231 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 173533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22674 grid for indexing accessible points = 1.400000 m= 89223 mr = 128375 m= 31701 mr = 73847 m= 7443 mr = 25886 m= 919 mr = 5754 m= 30 mr = 587 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 8465 time to turn everything in is 1.750000 number of dielectric boundary points 68400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 20432 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) : 1.858814 object centre at (A) : 51.21950 30.74100 48.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3042958 0.1197836 midg,1,midg; midg,igrid,midg 0.3285317 -0.8883385 1,midg,midg; igrid,midg,midg -0.1555048 1.019883 gauss-seidel spectral radius is 0.9992404 estimated iterations to convergence 286 setup time was (sec) 2.110000 now iterating at: 00:55:59 rms-change max change #iterations 9.747128 290.5679 at 10iterations 5.633577 151.4349 at 20iterations 3.238161 70.57275 at 30iterations 1.856257 41.87641 at 40iterations 1.065480 20.48629 at 50iterations 0.6074277 11.42947 at 60iterations 0.3476192 7.086136 at 70iterations 0.1987889 3.986092 at 80iterations 0.1132192 2.204326 at 90iterations 6.4846352E-02 1.320478 at 100iterations 3.7005056E-02 0.7457581 at 110iterations 2.1169947E-02 0.4019279 at 120iterations 1.2110215E-02 0.2407455 at 130iterations 6.9566425E-03 0.1444397 at 140iterations 4.0422394E-03 7.5462341E-02 at 150iterations 2.3799185E-03 5.1044464E-02 at 160iterations 1.4437110E-03 3.6354065E-02 at 170iterations 9.1209373E-04 2.0486832E-02 at 180iterations finished qdiffx linear iterations at : 00:56:12 total time elapsed so far: 14.77000 # loops : 180 mean,max change (kT/e) : 9.1209373E-04 2.0486832E-02 energy calculations done at 14.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.00000 DelPhi exited at 00:56:13 15.006u 0.248s 0:15.57 97.8% 0+0k 0+0io 0pf+0w