Mon Oct 10 09:26:08 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 Mon Oct 10 2011 at 09:26:08 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5990039 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 0.5990039 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5560 centred at (gu) : 89.82999 89.17107 90.49635 assigned negative charge : -285.5562 centred at (gu) : 89.81490 89.07518 90.61629 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4689 nv = 96 ne = 84 npr = 40453 no. pairs analyzed = 40453 no. exposed pairs = 2516 no. arc points = 17609 no. surface atoms = 854 nbur = 1104 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 211 mr = 2493 m= 2 mr = 19 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 0.2400000 number of dielectric boundary points 2390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1840 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6424549E-09 -1.1881004E-09 midg,1,midg; midg,igrid,midg -5.1608795E-10 3.8035579E-09 1,midg,midg; igrid,midg,midg 1.7889193E-09 2.4162525E-09 gauss-seidel spectral radius is 0.9855219 estimated iterations to convergence 68 setup time was (sec) 0.4600000 now iterating at: 09:26:09 rms-change max change #iterations 9.5243491E-02 16.32685 at 10iterations 7.8832433E-03 1.312799 at 20iterations 6.6804577E-04 0.1118088 at 30iterations 5.5130684E-05 9.6607208E-03 at 40iterations 4.7093481E-06 8.4686279E-04 at 50iterations finished qdiffx linear iterations at : 09:26:11 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 4.7093481E-06 8.4686279E-04 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 09:26:12 3.031u 0.136s 0:03.53 89.5% 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 Mon Oct 10 2011 at 09:26:12 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.797012 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 1.797012 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5560 centred at (gu) : 89.48979 87.51315 91.48913 assigned negative charge : -285.5562 centred at (gu) : 89.44460 87.22575 91.84885 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 51083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17609 grid for indexing accessible points = 1.400000 m= 16806 mr = 34551 m= 1959 mr = 12163 m= 97 mr = 1120 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 22087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14266 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) : 0.5990039 object centre at (A) : 20.98400 29.50300 17.27850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0579350E-02 -3.2383055E-04 midg,1,midg; midg,igrid,midg 1.1971974E-03 5.4987660E-03 1,midg,midg; igrid,midg,midg 3.6550894E-02 3.1571560E-02 gauss-seidel spectral radius is 0.9983917 estimated iterations to convergence 198 setup time was (sec) 0.6100000 now iterating at: 09:26:13 rms-change max change #iterations 3.206662 180.1859 at 10iterations 1.409576 54.70881 at 20iterations 0.6184087 23.36664 at 30iterations 0.2709427 11.13592 at 40iterations 0.1183352 4.565417 at 50iterations 5.1956516E-02 2.070124 at 60iterations 2.2854822E-02 0.8614302 at 70iterations 1.0044912E-02 0.3829455 at 80iterations 4.4062342E-03 0.1836586 at 90iterations 1.9197924E-03 6.8862200E-02 at 100iterations 8.4720529E-04 3.1454086E-02 at 110iterations 3.7165527E-04 1.7335892E-02 at 120iterations finished qdiffx linear iterations at : 09:26:19 total time elapsed so far: 6.510000 # loops : 120 mean,max change (kT/e) : 3.7165527E-04 1.7335892E-02 energy calculations done at 6.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.690000 DelPhi exited at 09:26:19 6.692u 0.166s 0:07.12 96.2% 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 Mon Oct 10 2011 at 09:26:19 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.695518 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): -8.731999 50.70000 ymin,ymax (A): 9.147000 49.85900 zmin,zma (A): -4.288000 38.84500 x,y,z range (A): 59.43200 40.71200 43.13300 scale (grids/A): 2.695518 object centre (A): 20.98400 29.50300 17.27850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 290.5560 centred at (gu) : 89.23464 86.26969 92.23366 assigned negative charge : -285.5562 centred at (gu) : 89.16702 85.83875 92.77329 start vw surface at 0.1300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 118026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17609 grid for indexing accessible points = 1.400000 m= 56271 mr = 83701 m= 17586 mr = 45564 m= 3126 mr = 13974 m= 377 mr = 2201 m= 16 mr = 216 m= 0 mr = 5 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 49741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14605 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) : 1.797012 object centre at (A) : 20.98400 29.50300 17.27850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1018222 2.0882821E-02 midg,1,midg; midg,igrid,midg 4.2553816E-02 4.3058537E-02 1,midg,midg; igrid,midg,midg 0.4512305 0.3235751 gauss-seidel spectral radius is 0.9991730 estimated iterations to convergence 275 setup time was (sec) 1.130000 now iterating at: 09:26:20 rms-change max change #iterations 7.823955 298.0978 at 10iterations 4.450844 135.8659 at 20iterations 2.505587 64.26433 at 30iterations 1.402989 34.07505 at 40iterations 0.7860107 18.81169 at 50iterations 0.4379291 10.06438 at 60iterations 0.2437365 5.581774 at 70iterations 0.1357622 3.102334 at 80iterations 7.5509049E-02 1.918674 at 90iterations 4.2096149E-02 0.9295654 at 100iterations 2.3393258E-02 0.5309601 at 110iterations 1.3023798E-02 0.2820972 at 120iterations 7.2215372E-03 0.1603928 at 130iterations 4.0167798E-03 9.2607498E-02 at 140iterations 2.2323932E-03 4.8606873E-02 at 150iterations 1.2379257E-03 2.7041435E-02 at 160iterations 6.8693259E-04 1.6742706E-02 at 170iterations 3.8173524E-04 8.3417892E-03 at 180iterations finished qdiffx linear iterations at : 09:26:30 total time elapsed so far: 10.27000 # loops : 180 mean,max change (kT/e) : 3.8173524E-04 8.3417892E-03 energy calculations done at 10.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.45000 DelPhi exited at 09:26:30 10.454u 0.166s 0:10.89 97.4% 0+0k 0+0io 0pf+0w