Tue Oct 11 04:20:27 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 Tue Oct 11 2011 at 04:20:27 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 43 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6607152 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): -10.88400 36.59700 ymin,ymax (A): 6.774000 55.77200 zmin,zma (A): -8.255000 45.62600 x,y,z range (A): 47.48100 48.99800 53.88100 scale (grids/A): 0.6607152 object centre (A): 12.85650 31.27300 18.68550 number of atom coordinates read : 2781 total number of charged atoms : 2612 net assigned charge : 3.514024 assigned positive charge : 423.3346 centred at (gu) : 89.93736 90.54400 91.60196 assigned negative charge : -419.8214 centred at (gu) : 89.68631 90.42023 91.63879 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 56447 no. pairs analyzed = 56447 no. exposed pairs = 3335 no. arc points = 23151 no. surface atoms = 1124 nbur = 1657 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 520 mr = 4735 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2161 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2385210E-08 1.3879446E-09 midg,1,midg; midg,igrid,midg -1.6045854E-08 4.0069708E-08 1,midg,midg; igrid,midg,midg -4.7491397E-08 6.1524972E-08 gauss-seidel spectral radius is 0.9881403 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 04:20:28 rms-change max change #iterations 0.1757389 23.97191 at 10iterations 1.9129600E-02 3.269939 at 20iterations 2.0958174E-03 0.2838554 at 30iterations 2.6788891E-04 4.1313171E-02 at 40iterations 5.0951883E-05 6.2541962E-03 at 50iterations finished qdiffx linear iterations at : 04:20:30 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 5.0951883E-05 6.2541962E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 04:20:31 3.228u 0.145s 0:03.92 85.7% 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 Tue Oct 11 2011 at 04:20:31 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 43 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: 1.982146 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): -10.88400 36.59700 ymin,ymax (A): 6.774000 55.77200 zmin,zma (A): -8.255000 45.62600 x,y,z range (A): 47.48100 48.99800 53.88100 scale (grids/A): 1.982146 object centre (A): 12.85650 31.27300 18.68550 number of atom coordinates read : 2781 total number of charged atoms : 2612 net assigned charge : 3.514024 assigned positive charge : 423.3346 centred at (gu) : 89.81129 91.63128 94.80542 assigned negative charge : -419.8214 centred at (gu) : 89.05850 91.26046 94.91618 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 35371 mr = 62499 m= 6468 mr = 27007 m= 480 mr = 4279 m= 6 mr = 205 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 35714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20651 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) : 0.6607152 object centre at (A) : 12.85650 31.27300 18.68550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4106930E-03 2.8273833E-03 midg,1,midg; midg,igrid,midg -8.9611774E-03 3.1307131E-02 1,midg,midg; igrid,midg,midg -1.7393537E-02 6.3366272E-02 gauss-seidel spectral radius is 0.9987504 estimated iterations to convergence 224 setup time was (sec) 0.8700000 now iterating at: 04:20:32 rms-change max change #iterations 4.811005 200.6616 at 10iterations 2.338960 72.61285 at 20iterations 1.131742 34.30678 at 30iterations 0.5474877 15.28712 at 40iterations 0.2665232 7.607680 at 50iterations 0.1294142 4.109666 at 60iterations 6.2622838E-02 1.913795 at 70iterations 3.0401070E-02 0.8168025 at 80iterations 1.4818131E-02 0.4040070 at 90iterations 7.1824533E-03 0.2134752 at 100iterations 3.5118419E-03 0.1084619 at 110iterations 1.7267055E-03 4.9030304E-02 at 120iterations finished qdiffx linear iterations at : 04:20:38 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.7267055E-03 4.9030304E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 04:20:39 7.088u 0.189s 0:07.84 92.6% 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 Tue Oct 11 2011 at 04:20:39 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 43 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: 2.973218 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): -10.88400 36.59700 ymin,ymax (A): 6.774000 55.77200 zmin,zma (A): -8.255000 45.62600 x,y,z range (A): 47.48100 48.99800 53.88100 scale (grids/A): 2.973218 object centre (A): 12.85650 31.27300 18.68550 number of atom coordinates read : 2781 total number of charged atoms : 2612 net assigned charge : 3.514024 assigned positive charge : 423.3346 centred at (gu) : 89.71680 92.44670 97.20815 assigned negative charge : -419.8214 centred at (gu) : 88.58767 91.89075 97.37422 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 201529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 110069 mr = 150219 m= 44739 mr = 91961 m= 11906 mr = 37036 m= 2016 mr = 9138 m= 172 mr = 1446 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 80560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 20896 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) : 1.982146 object centre at (A) : 12.85650 31.27300 18.68550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6915461E-02 0.3865801 midg,1,midg; midg,igrid,midg -0.1033963 0.3795196 1,midg,midg; igrid,midg,midg -0.1276350 0.5183010 gauss-seidel spectral radius is 0.9992865 estimated iterations to convergence 295 setup time was (sec) 1.880000 now iterating at: 04:20:41 rms-change max change #iterations 11.04207 390.1784 at 10iterations 6.497218 148.4783 at 20iterations 3.808600 72.16995 at 30iterations 2.232711 49.79549 at 40iterations 1.305068 24.86986 at 50iterations 0.7623417 14.14005 at 60iterations 0.4453458 8.834764 at 70iterations 0.2595227 4.194633 at 80iterations 0.1516275 2.819423 at 90iterations 8.8224702E-02 1.598068 at 100iterations 5.1363211E-02 0.9697380 at 110iterations 2.9891577E-02 0.5224867 at 120iterations 1.7451294E-02 0.3074527 at 130iterations 1.0174004E-02 0.1773033 at 140iterations 5.9519918E-03 9.6747875E-02 at 150iterations 3.4962706E-03 6.3848495E-02 at 160iterations 2.0724465E-03 3.4145355E-02 at 170iterations 1.2425896E-03 2.2148132E-02 at 180iterations finished qdiffx linear iterations at : 04:20:51 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 1.2425896E-03 2.2148132E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 04:20:51 11.762u 0.197s 0:12.56 95.1% 0+0k 0+0io 0pf+0w