Sat Oct 8 23:56:30 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 23:56:30 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6461566 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 0.6461566 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.01402 assigned positive charge : 356.4882 centred at (gu) : 89.82641 91.24501 90.81280 assigned negative charge : -344.4749 centred at (gu) : 89.77992 91.22562 90.74363 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6969 nv = 96 ne = 84 npr = 48374 no. pairs analyzed = 48374 no. exposed pairs = 3200 no. arc points = 23070 no. surface atoms = 1068 nbur = 1360 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3689 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0405890E-08 3.4461600E-08 midg,1,midg; midg,igrid,midg 1.4260741E-08 2.9853986E-08 1,midg,midg; igrid,midg,midg 1.5529588E-08 2.5415089E-08 gauss-seidel spectral radius is 0.9875827 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 23:56:31 rms-change max change #iterations 0.1419314 22.93366 at 10iterations 1.4455392E-02 2.012088 at 20iterations 1.6748140E-03 0.2220535 at 30iterations 3.2321876E-04 5.8626175E-02 at 40iterations 1.0355944E-04 2.0889282E-02 at 50iterations finished qdiffx linear iterations at : 23:56:34 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.0355944E-04 2.0889282E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 23:56:34 3.348u 0.161s 0:03.80 92.1% 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 23:56:34 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.938470 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 1.938470 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.01402 assigned positive charge : 356.4882 centred at (gu) : 89.47893 93.73434 92.43797 assigned negative charge : -344.4749 centred at (gu) : 89.33964 93.67664 92.23084 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 26736 mr = 50388 m= 4636 mr = 19319 m= 337 mr = 2867 m= 8 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 979 time to turn everything in is 0.3600000 number of dielectric boundary points 33698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18089 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) : 0.6461566 object centre at (A) : 13.54850 -3.582500 11.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3302214E-03 3.3802401E-02 midg,1,midg; midg,igrid,midg 3.9997596E-02 2.5610691E-02 1,midg,midg; igrid,midg,midg 5.5318512E-02 5.4709461E-02 gauss-seidel spectral radius is 0.9986722 estimated iterations to convergence 217 setup time was (sec) 0.5700000 now iterating at: 23:56:35 rms-change max change #iterations 4.105623 189.0089 at 10iterations 1.935026 70.58923 at 20iterations 0.9169691 29.12044 at 30iterations 0.4319233 16.40775 at 40iterations 0.2035561 6.572063 at 50iterations 9.6813127E-02 3.109924 at 60iterations 4.5755528E-02 1.410896 at 70iterations 2.1713465E-02 0.6627579 at 80iterations 1.0273055E-02 0.3097496 at 90iterations 4.9313228E-03 0.1590729 at 100iterations 2.3802498E-03 7.7167511E-02 at 110iterations 1.1873944E-03 4.1004181E-02 at 120iterations finished qdiffx linear iterations at : 23:56:42 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.1873944E-03 4.1004181E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 23:56:42 7.700u 0.200s 0:08.20 96.3% 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 23:56:43 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2428 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.907705 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): -13.99900 41.09600 ymin,ymax (A): -30.79700 23.63200 zmin,zma (A): -9.573000 32.62100 x,y,z range (A): 55.09500 54.42900 42.19400 scale (grids/A): 2.907705 object centre (A): 13.54850 -3.582500 11.52400 number of atom coordinates read : 2428 total number of charged atoms : 2293 net assigned charge : 12.01402 assigned positive charge : 356.4882 centred at (gu) : 89.21829 95.60140 93.65682 assigned negative charge : -344.4749 centred at (gu) : 89.00941 95.51491 93.34626 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 85779 mr = 122515 m= 31968 mr = 69014 m= 8349 mr = 25380 m= 1379 mr = 6249 m= 117 mr = 940 m= 4 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 3212 time to turn everything in is 0.9500000 number of dielectric boundary points 75920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18344 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) : 1.938470 object centre at (A) : 13.54850 -3.582500 11.52400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2723228E-03 0.3292767 midg,1,midg; midg,igrid,midg 0.5631434 0.2885451 1,midg,midg; igrid,midg,midg 0.5440029 0.5007051 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.180000 now iterating at: 23:56:44 rms-change max change #iterations 9.783504 659.6385 at 10iterations 5.787974 155.2603 at 20iterations 3.385088 82.06210 at 30iterations 1.980566 41.81230 at 40iterations 1.155329 24.07049 at 50iterations 0.6728145 13.20841 at 60iterations 0.3925475 7.657143 at 70iterations 0.2277923 4.802955 at 80iterations 0.1320165 2.488669 at 90iterations 7.6726735E-02 1.476035 at 100iterations 4.4465046E-02 0.7990513 at 110iterations 2.5807580E-02 0.5521874 at 120iterations 1.4958008E-02 0.2791729 at 130iterations 8.6843614E-03 0.1565552 at 140iterations 5.0616749E-03 9.4369888E-02 at 150iterations 2.9786841E-03 5.9151649E-02 at 160iterations 1.7803650E-03 3.5591125E-02 at 170iterations 1.0953218E-03 2.4124146E-02 at 180iterations finished qdiffx linear iterations at : 23:56:55 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 1.0953218E-03 2.4124146E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 23:56:56 12.580u 0.208s 0:13.05 97.9% 0+0k 0+0io 0pf+0w