Sat Oct 15 12:25:26 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 Sat Oct 15 2011 at 12:25:26 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6299324 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): 11.50100 68.01500 ymin,ymax (A): -26.88200 26.10700 zmin,zma (A): -6.889000 37.16100 x,y,z range (A): 56.51400 52.98900 44.05000 scale (grids/A): 0.6299324 object centre (A): 39.75800 -0.3874998 15.13600 number of atom coordinates read : 2098 total number of charged atoms : 1950 net assigned charge : -11.56598 assigned positive charge : 324.7564 centred at (gu) : 90.42142 89.38035 90.75262 assigned negative charge : -336.3229 centred at (gu) : 90.46718 89.11133 90.50508 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5736 nv = 96 ne = 84 npr = 41307 no. pairs analyzed = 41307 no. exposed pairs = 2913 no. arc points = 21313 no. surface atoms = 984 nbur = 1114 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2755 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1500000 number of dielectric boundary points 3259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2099 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6737 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7145632E-08 7.1349264E-09 midg,1,midg; midg,igrid,midg -3.8550372E-08 6.4469288E-09 1,midg,midg; igrid,midg,midg -8.2628278E-09 -1.7502446E-08 gauss-seidel spectral radius is 0.9869146 estimated iterations to convergence 72 setup time was (sec) 0.3400000 now iterating at: 12:25:26 rms-change max change #iterations 0.1274342 25.31492 at 10iterations 1.2137251E-02 2.091827 at 20iterations 1.3679314E-03 0.2461967 at 30iterations 2.5457778E-04 5.9766769E-02 at 40iterations 7.1769973E-05 1.7948151E-02 at 50iterations finished qdiffx linear iterations at : 12:25:29 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.1769973E-05 1.7948151E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:25:30 3.411u 0.210s 0:03.89 93.0% 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 Sat Oct 15 2011 at 12:25:30 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.889797 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): 11.50100 68.01500 ymin,ymax (A): -26.88200 26.10700 zmin,zma (A): -6.889000 37.16100 x,y,z range (A): 56.51400 52.98900 44.05000 scale (grids/A): 1.889797 object centre (A): 39.75800 -0.3874998 15.13600 number of atom coordinates read : 2098 total number of charged atoms : 1950 net assigned charge : -11.56598 assigned positive charge : 324.7564 centred at (gu) : 91.26411 88.14053 92.25764 assigned negative charge : -336.3229 centred at (gu) : 91.40160 87.33385 91.51529 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21313 grid for indexing accessible points = 1.400000 m= 20276 mr = 39354 m= 2928 mr = 13979 m= 163 mr = 1576 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.3200000 number of dielectric boundary points 29841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 15305 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) : 0.6299324 object centre at (A) : 39.75800 -0.3874998 15.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2382887E-02 8.1966417E-03 midg,1,midg; midg,igrid,midg -5.7161734E-02 3.1148627E-02 1,midg,midg; igrid,midg,midg -3.5948284E-02 -6.6538408E-02 gauss-seidel spectral radius is 0.9985750 estimated iterations to convergence 210 setup time was (sec) 0.5400000 now iterating at: 12:25:30 rms-change max change #iterations 3.865268 163.1190 at 10iterations 1.776269 67.70387 at 20iterations 0.8117920 31.70255 at 30iterations 0.3724948 13.83805 at 40iterations 0.1711803 7.012940 at 50iterations 7.8508280E-02 2.799274 at 60iterations 3.6027413E-02 1.264515 at 70iterations 1.6650872E-02 0.6473351 at 80iterations 7.7183070E-03 0.2757093 at 90iterations 3.6098217E-03 0.1295240 at 100iterations 1.7281190E-03 7.3940277E-02 at 110iterations 8.5392140E-04 3.7958145E-02 at 120iterations finished qdiffx linear iterations at : 12:25:38 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 8.5392140E-04 3.7958145E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 12:25:38 7.794u 0.204s 0:08.44 94.6% 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 Sat Oct 15 2011 at 12:25:38 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 has a net charge of 0.5140 !!! WARNING: HIR 136 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.834696 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): 11.50100 68.01500 ymin,ymax (A): -26.88200 26.10700 zmin,zma (A): -6.889000 37.16100 x,y,z range (A): 56.51400 52.98900 44.05000 scale (grids/A): 2.834696 object centre (A): 39.75800 -0.3874998 15.13600 number of atom coordinates read : 2098 total number of charged atoms : 1950 net assigned charge : -11.56598 assigned positive charge : 324.7564 centred at (gu) : 91.89602 87.21075 93.38626 assigned negative charge : -336.3229 centred at (gu) : 92.10245 86.00065 92.27292 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 141892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21313 grid for indexing accessible points = 1.400000 m= 66412 mr = 96209 m= 22312 mr = 52071 m= 4965 mr = 17012 m= 635 mr = 3351 m= 27 mr = 378 m= 0 mr = 3 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1392 time to turn everything in is 0.7600000 number of dielectric boundary points 67219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15600 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) : 1.889797 object centre at (A) : 39.75800 -0.3874998 15.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3093988 7.8837097E-02 midg,1,midg; midg,igrid,midg -0.7434243 0.2856412 1,midg,midg; igrid,midg,midg -0.5249967 -0.8893000 gauss-seidel spectral radius is 0.9992408 estimated iterations to convergence 286 setup time was (sec) 1.000000 now iterating at: 12:25:39 rms-change max change #iterations 9.174556 326.1719 at 10iterations 5.315120 121.7365 at 20iterations 3.059132 67.11224 at 30iterations 1.761472 42.82890 at 40iterations 1.006463 20.51950 at 50iterations 0.5747969 12.91079 at 60iterations 0.3288327 6.616098 at 70iterations 0.1875921 3.741082 at 80iterations 0.1069223 2.364126 at 90iterations 6.1052941E-02 1.214899 at 100iterations 3.4856487E-02 0.7192574 at 110iterations 1.9909849E-02 0.4054279 at 120iterations 1.1397989E-02 0.2768526 at 130iterations 6.5824431E-03 0.1435061 at 140iterations 3.8208468E-03 7.7930450E-02 at 150iterations 2.2780914E-03 4.8163414E-02 at 160iterations 1.3953981E-03 3.5095215E-02 at 170iterations 8.9774403E-04 2.4192810E-02 at 180iterations finished qdiffx linear iterations at : 12:25:50 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 8.9774403E-04 2.4192810E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 12:25:51 12.291u 0.208s 0:12.93 96.5% 0+0k 0+0io 0pf+0w