Mon Oct 10 16:26:30 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 16:26:30 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 !!! WARNING: GLM 80 has a net charge of -0.0940 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: 0.6151720 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 0.6151720 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2279 net assigned charge : 9.906016 assigned positive charge : 365.6149 centred at (gu) : 89.43853 88.65862 90.67600 assigned negative charge : -355.7096 centred at (gu) : 89.58218 88.56503 90.74231 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6185 nv = 96 ne = 84 npr = 46959 no. pairs analyzed = 46959 no. exposed pairs = 3357 no. arc points = 23892 no. surface atoms = 1119 nbur = 1304 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3051 m= 6 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2431 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7584 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9705905E-09 3.8933514E-09 midg,1,midg; midg,igrid,midg 2.4695819E-09 8.8175556E-09 1,midg,midg; igrid,midg,midg 1.6277186E-08 -6.5049399E-10 gauss-seidel spectral radius is 0.9863126 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 16:26:30 rms-change max change #iterations 0.1172108 20.40087 at 10iterations 1.0429927E-02 1.758154 at 20iterations 9.3034812E-04 0.1569471 at 30iterations 8.4315609E-05 1.2025833E-02 at 40iterations 7.7403220E-06 1.1806488E-03 at 50iterations finished qdiffx linear iterations at : 16:26:33 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 7.7403220E-06 1.1806488E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:26:34 3.568u 0.186s 0:04.03 92.8% 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 Mon Oct 10 2011 at 16:26:34 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 !!! WARNING: GLM 80 has a net charge of -0.0940 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: 1.845516 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 1.845516 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2279 net assigned charge : 9.906016 assigned positive charge : 365.6149 centred at (gu) : 88.31503 85.97529 92.02760 assigned negative charge : -355.7096 centred at (gu) : 88.74641 85.69501 92.22676 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 66329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 22854 mr = 42945 m= 3358 mr = 15943 m= 148 mr = 1846 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 31927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17847 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) : 0.6151720 object centre at (A) : 230.8755 86.26900 186.6590 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0247487E-02 3.0835511E-02 midg,1,midg; midg,igrid,midg -5.9600952E-03 1.1892735E-02 1,midg,midg; igrid,midg,midg 3.1080084E-02 1.1021824E-02 gauss-seidel spectral radius is 0.9985408 estimated iterations to convergence 208 setup time was (sec) 0.8400000 now iterating at: 16:26:35 rms-change max change #iterations 3.815392 168.2846 at 10iterations 1.729882 60.61768 at 20iterations 0.7901859 29.31255 at 30iterations 0.3590584 12.16751 at 40iterations 0.1639658 5.828243 at 50iterations 7.4399501E-02 2.680243 at 60iterations 3.3914462E-02 1.184622 at 70iterations 1.5403093E-02 0.5353746 at 80iterations 7.0517715E-03 0.2394514 at 90iterations 3.2081574E-03 0.1116676 at 100iterations 1.4671605E-03 5.3359985E-02 at 110iterations 6.6805928E-04 2.4475098E-02 at 120iterations finished qdiffx linear iterations at : 16:26:42 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 6.6805928E-04 2.4475098E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 16:26:43 7.942u 0.208s 0:08.72 93.3% 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 Mon Oct 10 2011 at 16:26:43 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 !!! WARNING: GLM 80 has a net charge of -0.0940 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: 2.768274 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 2.768274 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2279 net assigned charge : 9.906016 assigned positive charge : 365.6149 centred at (gu) : 87.47253 83.96295 93.04121 assigned negative charge : -355.7096 centred at (gu) : 88.11955 83.54248 93.34009 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 73919 mr = 105220 m= 25944 mr = 58092 m= 5792 mr = 19977 m= 731 mr = 3961 m= 23 mr = 405 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 72099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18228 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) : 1.845516 object centre at (A) : 230.8755 86.26900 186.6590 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5608808 0.2719817 midg,1,midg; midg,igrid,midg -6.6250801E-02 0.1122387 1,midg,midg; igrid,midg,midg 0.2548766 0.1294515 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.610000 now iterating at: 16:26:44 rms-change max change #iterations 9.222387 300.4824 at 10iterations 5.399668 126.5310 at 20iterations 3.113613 78.74120 at 30iterations 1.794851 37.59036 at 40iterations 1.031183 23.60442 at 50iterations 0.5892162 12.50131 at 60iterations 0.3358006 6.932201 at 70iterations 0.1920008 3.817589 at 80iterations 0.1094543 2.178177 at 90iterations 6.2343422E-02 1.294966 at 100iterations 3.5524119E-02 0.6778016 at 110iterations 2.0277696E-02 0.4016647 at 120iterations 1.1535576E-02 0.2206955 at 130iterations 6.5778843E-03 0.1307397 at 140iterations 3.7365544E-03 7.6536179E-02 at 150iterations 2.1317059E-03 4.2770386E-02 at 160iterations 1.2103320E-03 2.4912357E-02 at 170iterations 6.9013803E-04 1.3702393E-02 at 180iterations finished qdiffx linear iterations at : 16:26:55 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 6.9013803E-04 1.3702393E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 16:26:56 12.790u 0.234s 0:13.38 97.3% 0+0k 0+0io 0pf+0w