Sat Oct 8 13:32:07 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 8 2011 at 13:32:08 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 0.6364986 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 0.6364986 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 8.1211329E-06 assigned positive charge : 446.5306 centred at (gu) : 88.75111 89.01199 87.51613 assigned negative charge : -446.5314 centred at (gu) : 88.70782 88.99255 87.61130 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8019 nv = 96 ne = 84 npr = 61660 no. pairs analyzed = 61660 no. exposed pairs = 3841 no. arc points = 26201 no. surface atoms = 1292 nbur = 1696 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4386 m= 3 mr = 70 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 0.3100000 number of dielectric boundary points 4035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9866 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9402384E-08 -6.9157551E-09 midg,1,midg; midg,igrid,midg -3.1921854E-09 1.7150227E-09 1,midg,midg; igrid,midg,midg -7.2054371E-09 3.8011314E-09 gauss-seidel spectral radius is 0.9872452 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 13:32:08 rms-change max change #iterations 0.1572352 23.67376 at 10iterations 1.6000763E-02 2.200882 at 20iterations 1.9530604E-03 0.2409477 at 30iterations 4.9627526E-04 6.5605164E-02 at 40iterations 1.8718722E-04 2.3403168E-02 at 50iterations finished qdiffx linear iterations at : 13:32:11 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.8718722E-04 2.3403168E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 13:32:11 3.123u 0.151s 0:03.58 91.3% 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 13:32:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 1.909496 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 1.909496 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 8.1211329E-06 assigned positive charge : 446.5306 centred at (gu) : 86.25245 87.03560 82.54766 assigned negative charge : -446.5314 centred at (gu) : 86.12301 86.97740 82.83362 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26201 grid for indexing accessible points = 1.400000 m= 33155 mr = 60093 m= 6022 mr = 24332 m= 361 mr = 3761 m= 6 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22375 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) : 0.6364986 object centre at (A) : 1.931000 1.047999 4.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4640681E-02 -2.9187931E-02 midg,1,midg; midg,igrid,midg 1.9173799E-02 1.3372044E-02 1,midg,midg; igrid,midg,midg -1.5344277E-02 -4.3840441E-03 gauss-seidel spectral radius is 0.9986786 estimated iterations to convergence 218 setup time was (sec) 0.8900000 now iterating at: 13:32:12 rms-change max change #iterations 4.670213 196.2693 at 10iterations 2.206694 72.75305 at 20iterations 1.044729 29.39046 at 30iterations 0.4961529 14.15191 at 40iterations 0.2348257 7.171220 at 50iterations 0.1117083 3.336351 at 60iterations 5.3239744E-02 1.616165 at 70iterations 2.5422804E-02 0.7659702 at 80iterations 1.2172007E-02 0.3963089 at 90iterations 5.9352661E-03 0.1922169 at 100iterations 2.9732734E-03 9.1663361E-02 at 110iterations 1.5631081E-03 4.9560547E-02 at 120iterations finished qdiffx linear iterations at : 13:32:18 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.5631081E-03 4.9560547E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 13:32:19 7.008u 0.149s 0:07.43 96.0% 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 13:32:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: NAP 350 has a net charge of -2.0000 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: 2.864244 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): -23.50200 27.36400 ymin,ymax (A): -25.14600 27.24200 zmin,zma (A): -23.02800 32.90300 x,y,z range (A): 50.86600 52.38800 55.93100 scale (grids/A): 2.864244 object centre (A): 1.931000 1.047999 4.937500 number of atom coordinates read : 2988 total number of charged atoms : 2842 net assigned charge : 8.1211329E-06 assigned positive charge : 446.5306 centred at (gu) : 84.37849 85.55340 78.82147 assigned negative charge : -446.5314 centred at (gu) : 84.18450 85.46613 79.25037 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 199180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26201 grid for indexing accessible points = 1.400000 m= 104295 mr = 145876 m= 40702 mr = 84914 m= 11075 mr = 32649 m= 1645 mr = 8199 m= 77 mr = 1032 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 84285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22736 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) : 1.909496 object centre at (A) : 1.931000 1.047999 4.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4821634 -0.3336499 midg,1,midg; midg,igrid,midg 0.2190362 0.1259129 1,midg,midg; igrid,midg,midg -7.0488788E-02 4.7454983E-03 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 13:32:21 rms-change max change #iterations 10.93528 419.8141 at 10iterations 6.483299 140.8150 at 20iterations 3.829777 80.81242 at 30iterations 2.255667 49.40865 at 40iterations 1.324394 26.72689 at 50iterations 0.7742150 15.20491 at 60iterations 0.4533573 8.235857 at 70iterations 0.2640996 4.696671 at 80iterations 0.1540841 2.388483 at 90iterations 8.9727841E-02 1.685067 at 100iterations 5.2134681E-02 0.8906555 at 110iterations 3.0326590E-02 0.4743633 at 120iterations 1.7628465E-02 0.2892747 at 130iterations 1.0270257E-02 0.1747131 at 140iterations 5.9901294E-03 9.9494934E-02 at 150iterations 3.5051005E-03 5.5151939E-02 at 160iterations 2.0628942E-03 3.6663055E-02 at 170iterations 1.2339941E-03 2.1053314E-02 at 180iterations finished qdiffx linear iterations at : 13:32:30 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 1.2339941E-03 2.1053314E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 13:32:31 11.891u 0.189s 0:12.34 97.8% 0+0k 0+0io 0pf+0w