Tue Oct 11 08:19:40 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 Tue Oct 11 2011 at 08:19:40 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7384207 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 0.7384207 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 174.1781 centred at (gu) : 88.66513 89.00242 88.75025 assigned negative charge : -168.6781 centred at (gu) : 88.35337 88.97990 88.77707 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4385 nv = 96 ne = 84 npr = 21960 no. pairs analyzed = 21960 no. exposed pairs = 1505 no. arc points = 11149 no. surface atoms = 502 nbur = 645 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2271 m= 0 mr = 51 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 979 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3803457E-07 6.5740238E-08 midg,1,midg; midg,igrid,midg 1.0089880E-07 8.9767958E-08 1,midg,midg; igrid,midg,midg -9.2464553E-08 1.9656225E-07 gauss-seidel spectral radius is 0.9903479 estimated iterations to convergence 83 setup time was (sec) 0.3000000 now iterating at: 08:19:41 rms-change max change #iterations 0.1705812 29.13630 at 10iterations 2.2599857E-02 4.706139 at 20iterations 2.9556404E-03 0.5392895 at 30iterations 3.8938940E-04 6.9320679E-02 at 40iterations 5.2126870E-05 8.7804794E-03 at 50iterations finished qdiffx linear iterations at : 08:19:44 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 5.2126870E-05 8.7804794E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 08:19:44 3.231u 0.163s 0:03.78 89.6% 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 08:19:44 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.215262 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 2.215262 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 174.1781 centred at (gu) : 85.99554 87.00728 86.25081 assigned negative charge : -168.6781 centred at (gu) : 85.06025 86.93990 86.33134 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11149 grid for indexing accessible points = 1.400000 m= 17609 mr = 29356 m= 3628 mr = 13138 m= 370 mr = 2535 m= 22 mr = 224 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 21704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8436 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) : 0.7384207 object centre at (A) : 12.98200 20.96200 22.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7556773E-02 3.6672372E-03 midg,1,midg; midg,igrid,midg 3.7879352E-02 3.1424295E-02 1,midg,midg; igrid,midg,midg -2.8979298E-02 3.9037142E-02 gauss-seidel spectral radius is 0.9988303 estimated iterations to convergence 231 setup time was (sec) 0.4500000 now iterating at: 08:19:45 rms-change max change #iterations 3.545274 231.3290 at 10iterations 1.757958 70.82193 at 20iterations 0.8650180 35.27221 at 30iterations 0.4322798 17.18085 at 40iterations 0.2111670 8.043289 at 50iterations 0.1043262 4.297649 at 60iterations 5.1430363E-02 1.948478 at 70iterations 2.5390362E-02 1.008248 at 80iterations 1.2557820E-02 0.4492950 at 90iterations 6.2292912E-03 0.2251110 at 100iterations 3.0791811E-03 0.1234794 at 110iterations 1.5176747E-03 6.0638428E-02 at 120iterations finished qdiffx linear iterations at : 08:19:52 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.5176747E-03 6.0638428E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:19:52 7.611u 0.202s 0:08.32 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 Tue Oct 11 2011 at 08:19:52 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1147 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.322893 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): -6.477000 32.44100 ymin,ymax (A): 0.8249999 41.09900 zmin,zma (A): -2.063000 46.14800 x,y,z range (A): 38.91800 40.27400 48.21100 scale (grids/A): 3.322893 object centre (A): 12.98200 20.96200 22.04250 number of atom coordinates read : 1147 total number of charged atoms : 1058 net assigned charge : 5.500003 assigned positive charge : 174.1781 centred at (gu) : 83.99345 85.51096 84.37627 assigned negative charge : -168.6781 centred at (gu) : 82.59042 85.40991 84.49711 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 104261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11149 grid for indexing accessible points = 1.400000 m= 53627 mr = 71002 m= 22736 mr = 43683 m= 6920 mr = 18718 m= 1483 mr = 5567 m= 220 mr = 1146 m= 25 mr = 172 m= 0 mr = 23 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 48961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 8464 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) : 2.215262 object centre at (A) : 12.98200 20.96200 22.04250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3304419 1.9230410E-02 midg,1,midg; midg,igrid,midg 0.3398503 0.2759353 1,midg,midg; igrid,midg,midg -0.2262777 0.2885366 gauss-seidel spectral radius is 0.9992947 estimated iterations to convergence 297 setup time was (sec) 0.9400000 now iterating at: 08:19:54 rms-change max change #iterations 7.811282 271.0647 at 10iterations 4.551762 132.5933 at 20iterations 2.642658 65.07629 at 30iterations 1.525835 39.01835 at 40iterations 0.8871821 19.64626 at 50iterations 0.5144233 10.42914 at 60iterations 0.2986208 6.782015 at 70iterations 0.1735282 3.706095 at 80iterations 0.1004018 2.119910 at 90iterations 5.8032181E-02 1.251574 at 100iterations 3.3697177E-02 0.7132324 at 110iterations 1.9504704E-02 0.4171150 at 120iterations 1.1326887E-02 0.2402344 at 130iterations 6.5756310E-03 0.1533394 at 140iterations 3.8222754E-03 8.0681264E-02 at 150iterations 2.2184686E-03 4.5532227E-02 at 160iterations 1.2852725E-03 2.6606321E-02 at 170iterations 7.4564014E-04 1.5983582E-02 at 180iterations finished qdiffx linear iterations at : 08:20:04 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 7.4564014E-04 1.5983582E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 08:20:05 11.786u 0.202s 0:12.32 97.2% 0+0k 0+0io 0pf+0w