Sat Oct 15 12:25:00 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 15 2011 at 12:25:00 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-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 : 1954 net assigned charge : -11.49999 assigned positive charge : 320.6325 centred at (gu) : 90.38647 89.32294 90.75862 assigned negative charge : -332.1329 centred at (gu) : 90.44199 89.05874 90.50389 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-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 = 6.9999993E-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 = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1700000 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 0.2400000 number of grid points assigned charge 6743 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7322486E-08 7.5726607E-09 midg,1,midg; midg,igrid,midg -3.8189434E-08 5.9168626E-09 1,midg,midg; igrid,midg,midg -7.6199882E-09 -1.8051123E-08 gauss-seidel spectral radius is 0.9869146 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 12:25:00 rms-change max change #iterations 0.1224532 24.00488 at 10iterations 1.1625548E-02 1.870989 at 20iterations 1.3156323E-03 0.2332325 at 30iterations 2.4690403E-04 5.8027267E-02 at 40iterations 6.9684102E-05 1.7423630E-02 at 50iterations finished qdiffx linear iterations at : 12:25:03 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.9684102E-05 1.7423630E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:25:04 3.475u 0.179s 0:04.01 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 15 2011 at 12:25:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 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 : 1954 net assigned charge : -11.49999 assigned positive charge : 320.6325 centred at (gu) : 91.15925 87.96839 92.27570 assigned negative charge : -332.1329 centred at (gu) : 91.32604 87.17609 91.51171 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 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 = 0.1300000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.3000000 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 0.3700000 number of grid points assigned charge 15336 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 -3.2703198E-02 9.0330346E-03 midg,1,midg; midg,igrid,midg -5.6760296E-02 3.0263828E-02 1,midg,midg; igrid,midg,midg -3.4913626E-02 -6.7189708E-02 gauss-seidel spectral radius is 0.9985750 estimated iterations to convergence 210 setup time was (sec) 0.5000000 now iterating at: 12:25:05 rms-change max change #iterations 3.803140 163.1190 at 10iterations 1.744941 63.19010 at 20iterations 0.7984402 30.73934 at 30iterations 0.3659140 13.86042 at 40iterations 0.1681889 6.565666 at 50iterations 7.7180259E-02 2.657536 at 60iterations 3.5388097E-02 1.233341 at 70iterations 1.6370589E-02 0.6274719 at 80iterations 7.5781313E-03 0.2721586 at 90iterations 3.5455704E-03 0.1226807 at 100iterations 1.6967064E-03 7.2395802E-02 at 110iterations 8.3804555E-04 3.6958694E-02 at 120iterations finished qdiffx linear iterations at : 12:25:12 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 8.3804555E-04 3.6958694E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 12:25:12 7.692u 0.218s 0:08.44 93.6% 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 12:25:12 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2098 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 : 1954 net assigned charge : -11.49999 assigned positive charge : 320.6325 centred at (gu) : 91.73875 86.95255 93.41336 assigned negative charge : -332.1329 centred at (gu) : 91.98911 85.76403 92.26754 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 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 = 0.4300000 no. cavity mid-points inaccessible to solvent = 1392 time to turn everything in is 0.7800000 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 0.8700000 number of grid points assigned charge 15632 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 -0.3135324 8.7771676E-02 midg,1,midg; midg,igrid,midg -0.7393201 0.2784789 1,midg,midg; igrid,midg,midg -0.5130702 -0.8966957 gauss-seidel spectral radius is 0.9992408 estimated iterations to convergence 286 setup time was (sec) 1.030000 now iterating at: 12:25:14 rms-change max change #iterations 9.032024 326.1628 at 10iterations 5.235333 120.6579 at 20iterations 3.014626 64.16582 at 30iterations 1.736656 43.46277 at 40iterations 0.9923304 20.53068 at 50iterations 0.5668793 12.65595 at 60iterations 0.3243110 6.516052 at 70iterations 0.1850404 3.850113 at 80iterations 0.1054778 2.459137 at 90iterations 6.0219467E-02 1.178691 at 100iterations 3.4395479E-02 0.7160072 at 110iterations 1.9644232E-02 0.4059486 at 120iterations 1.1244565E-02 0.2662010 at 130iterations 6.4945053E-03 0.1430721 at 140iterations 3.7672515E-03 7.6934814E-02 at 150iterations 2.2435952E-03 4.8439026E-02 at 160iterations 1.3716341E-03 3.4118652E-02 at 170iterations 8.8094681E-04 2.4024963E-02 at 180iterations finished qdiffx linear iterations at : 12:25:25 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 8.8094681E-04 2.4024963E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 12:25:26 12.462u 0.234s 0:13.05 97.2% 0+0k 0+0io 0pf+0w