Sat Oct 8 20:25:44 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 8 2011 at 20:25:44 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6300885 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 0.6300885 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 88.58794 89.28126 89.94113 assigned negative charge : -391.6796 centred at (gu) : 88.48124 89.31326 89.83716 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 54010 no. pairs analyzed = 54010 no. exposed pairs = 3040 no. arc points = 21933 no. surface atoms = 1017 nbur = 1570 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3737 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.2900000 number of dielectric boundary points 3292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2195 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9117328E-09 1.3540806E-08 midg,1,midg; midg,igrid,midg 8.6244345E-09 1.4619824E-09 1,midg,midg; igrid,midg,midg -7.0865331E-09 1.0289526E-08 gauss-seidel spectral radius is 0.9869481 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 20:25:44 rms-change max change #iterations 0.1358227 19.05487 at 10iterations 1.3148242E-02 2.362991 at 20iterations 1.2726472E-03 0.1954517 at 30iterations 1.2133461E-04 1.8775940E-02 at 40iterations 1.1865978E-05 1.5296936E-03 at 50iterations finished qdiffx linear iterations at : 20:25:47 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.1865978E-05 1.5296936E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 20:25:47 3.109u 0.125s 0:03.55 90.7% 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 Sat Oct 8 2011 at 20:25:47 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.890265 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 1.890265 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 85.76310 87.84310 89.82275 assigned negative charge : -391.6796 centred at (gu) : 85.44360 87.93955 89.51129 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21933 grid for indexing accessible points = 1.400000 m= 25454 mr = 50857 m= 3789 mr = 18813 m= 209 mr = 2301 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4026 time to turn everything in is 0.5000000 number of dielectric boundary points 30276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19349 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) : 0.6300885 object centre at (A) : 14.08300 1.252500 15.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8969147E-02 2.4731304E-02 midg,1,midg; midg,igrid,midg 1.3930290E-02 5.2192686E-03 1,midg,midg; igrid,midg,midg -3.6824837E-03 3.5083130E-02 gauss-seidel spectral radius is 0.9986102 estimated iterations to convergence 213 setup time was (sec) 0.7600000 now iterating at: 20:25:48 rms-change max change #iterations 4.154592 174.9215 at 10iterations 1.933734 62.53312 at 20iterations 0.8967287 32.93590 at 30iterations 0.4173707 13.08536 at 40iterations 0.1948007 6.271149 at 50iterations 9.0815842E-02 3.123425 at 60iterations 4.2022794E-02 1.355331 at 70iterations 1.9607166E-02 0.6283455 at 80iterations 9.1298791E-03 0.2844334 at 90iterations 4.2492002E-03 0.1324768 at 100iterations 1.9829504E-03 6.1983585E-02 at 110iterations 9.1998570E-04 2.9743195E-02 at 120iterations finished qdiffx linear iterations at : 20:25:54 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 9.1998570E-04 2.9743195E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 20:25:55 6.917u 0.173s 0:07.37 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 Sat Oct 8 2011 at 20:25:55 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2587 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.835398 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): -10.43000 38.59600 ymin,ymax (A): -22.17000 24.67500 zmin,zma (A): -12.48800 44.01200 x,y,z range (A): 49.02600 46.84500 56.50000 scale (grids/A): 2.835398 object centre (A): 14.08300 1.252500 15.76200 number of atom coordinates read : 2587 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 83.64444 86.76456 89.73403 assigned negative charge : -391.6796 centred at (gu) : 83.16532 86.90926 89.26675 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 168663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21933 grid for indexing accessible points = 1.400000 m= 83902 mr = 122994 m= 28736 mr = 69162 m= 6714 mr = 22901 m= 851 mr = 5007 m= 48 mr = 538 m= 0 mr = 17 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 13282 time to turn everything in is 1.230000 number of dielectric boundary points 68295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19718 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) : 1.890265 object centre at (A) : 14.08300 1.252500 15.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1302299 0.2740550 midg,1,midg; midg,igrid,midg 0.1601049 6.0544889E-02 1,midg,midg; igrid,midg,midg -1.3058167E-02 0.4338086 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.510000 now iterating at: 20:25:56 rms-change max change #iterations 9.796081 395.2074 at 10iterations 5.673216 134.0315 at 20iterations 3.263888 67.06311 at 30iterations 1.872904 40.90604 at 40iterations 1.074528 20.79608 at 50iterations 0.6151574 13.34763 at 60iterations 0.3521213 6.287720 at 70iterations 0.2020782 3.897702 at 80iterations 0.1157137 2.334829 at 90iterations 6.5919824E-02 1.177631 at 100iterations 3.7861001E-02 0.6895657 at 110iterations 2.1570172E-02 0.3995705 at 120iterations 1.2379938E-02 0.2255049 at 130iterations 7.0729475E-03 0.1319065 at 140iterations 4.0445528E-03 7.5027466E-02 at 150iterations 2.3132234E-03 4.2587280E-02 at 160iterations 1.3258953E-03 2.2696137E-02 at 170iterations 7.6163415E-04 1.5171051E-02 at 180iterations finished qdiffx linear iterations at : 20:26:06 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 7.6163415E-04 1.5171051E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 20:26:06 11.172u 0.188s 0:11.62 97.6% 0+0k 0+0io 0pf+0w