Sat Oct 8 11:36:49 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 Sat Oct 8 2011 at 11:36:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 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: 0.6313176 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 0.6313176 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.499973 assigned positive charge : 510.3983 centred at (gu) : 89.46952 89.37904 91.03292 assigned negative charge : -514.8994 centred at (gu) : 89.29073 89.49443 91.01801 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8711 nv = 96 ne = 84 npr = 71480 no. pairs analyzed = 71480 no. exposed pairs = 3723 no. arc points = 25494 no. surface atoms = 1276 nbur = 2080 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 5258 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5144631E-09 -3.9851433E-09 midg,1,midg; midg,igrid,midg 1.0155312E-08 -1.6822195E-08 1,midg,midg; igrid,midg,midg -3.0579617E-08 1.4454994E-08 gauss-seidel spectral radius is 0.9870564 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 11:36:50 rms-change max change #iterations 0.1633015 21.68322 at 10iterations 1.5698871E-02 2.165054 at 20iterations 1.5364682E-03 0.2131858 at 30iterations 1.5272974E-04 2.0402908E-02 at 40iterations 1.5462962E-05 1.8711090E-03 at 50iterations finished qdiffx linear iterations at : 11:36:53 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.5462962E-05 1.8711090E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 11:36:53 3.183u 0.139s 0:03.59 92.2% 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 Sat Oct 8 2011 at 11:36:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 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: 1.893953 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 1.893953 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.499973 assigned positive charge : 510.3983 centred at (gu) : 88.40786 88.13633 93.09773 assigned negative charge : -514.8994 centred at (gu) : 87.87153 88.48266 93.05332 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 94261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 grid for indexing accessible points = 1.400000 m= 36768 mr = 68676 m= 6045 mr = 28938 m= 352 mr = 4062 m= 3 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1316 time to turn everything in is 0.6400000 number of dielectric boundary points 35615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 25174 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) : 0.6313176 object centre at (A) : 59.34950 53.94100 21.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5989196E-02 -3.4925599E-02 midg,1,midg; midg,igrid,midg 2.9149737E-02 -2.7562538E-02 1,midg,midg; igrid,midg,midg -4.9517438E-02 7.1918388E-05 gauss-seidel spectral radius is 0.9986764 estimated iterations to convergence 218 setup time was (sec) 0.9000000 now iterating at: 11:36:54 rms-change max change #iterations 4.941507 173.4991 at 10iterations 2.343062 71.85320 at 20iterations 1.113444 33.21811 at 30iterations 0.5287795 15.23047 at 40iterations 0.2498781 7.525423 at 50iterations 0.1184661 3.323357 at 60iterations 5.6388374E-02 1.510830 at 70iterations 2.6809948E-02 0.7809238 at 80iterations 1.2736835E-02 0.3457508 at 90iterations 6.0514803E-03 0.2043800 at 100iterations 2.8747406E-03 8.4698677E-02 at 110iterations 1.3638193E-03 3.9640427E-02 at 120iterations finished qdiffx linear iterations at : 11:37:00 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 1.3638193E-03 3.9640427E-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 11:37:01 7.032u 0.173s 0:07.67 93.8% 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 Sat Oct 8 2011 at 11:37:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 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: 2.840929 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 2.840929 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.499973 assigned positive charge : 510.3983 centred at (gu) : 87.61146 87.20429 94.64629 assigned negative charge : -514.8994 centred at (gu) : 86.80738 87.72375 94.57977 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 218000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 grid for indexing accessible points = 1.400000 m= 117088 mr = 165248 m= 44956 mr = 99531 m= 11251 mr = 37903 m= 1580 mr = 8776 m= 82 mr = 1089 m= 0 mr = 38 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 4295 time to turn everything in is 1.610000 number of dielectric boundary points 80372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 25628 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) : 1.893953 object centre at (A) : 59.34950 53.94100 21.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1878742 -0.3178759 midg,1,midg; midg,igrid,midg 0.5580311 1.6479868E-02 1,midg,midg; igrid,midg,midg -0.5426895 -0.2894626 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.890000 now iterating at: 11:37:03 rms-change max change #iterations 11.41578 275.2212 at 10iterations 6.689479 138.3182 at 20iterations 3.890644 71.09842 at 30iterations 2.254147 40.66381 at 40iterations 1.309479 24.05756 at 50iterations 0.7603617 12.85031 at 60iterations 0.4393660 7.485674 at 70iterations 0.2537614 4.267616 at 80iterations 0.1469292 2.845566 at 90iterations 8.4664680E-02 1.391663 at 100iterations 4.8957869E-02 0.8764781 at 110iterations 2.8326232E-02 0.4343872 at 120iterations 1.6361231E-02 0.2516472 at 130iterations 9.4572054E-03 0.1461449 at 140iterations 5.4681236E-03 8.0615997E-02 at 150iterations 3.1597298E-03 4.8339844E-02 at 160iterations 1.8279515E-03 2.9115677E-02 at 170iterations 1.0555132E-03 1.6710281E-02 at 180iterations finished qdiffx linear iterations at : 11:37:12 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 1.0555132E-03 1.6710281E-02 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 11:37:13 11.693u 0.190s 0:12.16 97.6% 0+0k 0+0io 0pf+0w