Mon Oct 10 14:39:22 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 14:39:22 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6555203 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 0.6555203 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.9852 centred at (gu) : 90.28989 89.32787 90.28661 assigned negative charge : -362.4858 centred at (gu) : 90.10294 89.34387 90.35606 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6887 nv = 96 ne = 84 npr = 48813 no. pairs analyzed = 48813 no. exposed pairs = 3000 no. arc points = 20972 no. surface atoms = 1026 nbur = 1338 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3761 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2029 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2000205E-09 -2.0643483E-08 midg,1,midg; midg,igrid,midg -6.0397585E-09 -9.2081560E-09 1,midg,midg; igrid,midg,midg -3.6989526E-08 2.3702356E-08 gauss-seidel spectral radius is 0.9879221 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 14:39:22 rms-change max change #iterations 0.1585658 30.54589 at 10iterations 1.6431641E-02 2.095332 at 20iterations 1.8175486E-03 0.2739944 at 30iterations 2.8292110E-04 3.9705276E-02 at 40iterations 7.1575341E-05 1.1535645E-02 at 50iterations finished qdiffx linear iterations at : 14:39:25 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 7.1575341E-05 1.1535645E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:39:26 3.293u 0.183s 0:04.55 76.2% 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 14:39:26 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.966561 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 1.966561 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.9852 centred at (gu) : 90.86918 87.98308 90.85950 assigned negative charge : -362.4858 centred at (gu) : 90.30868 88.03151 91.06802 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20972 grid for indexing accessible points = 1.400000 m= 27735 mr = 51190 m= 4984 mr = 20462 m= 383 mr = 3133 m= 2 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 32184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17638 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) : 0.6555203 object centre at (A) : 44.68700 49.58200 53.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6967511E-02 -3.5813428E-02 midg,1,midg; midg,igrid,midg -1.7408661E-03 -1.1883087E-02 1,midg,midg; igrid,midg,midg -7.9150703E-03 3.0457852E-02 gauss-seidel spectral radius is 0.9987003 estimated iterations to convergence 220 setup time was (sec) 0.8200000 now iterating at: 14:39:27 rms-change max change #iterations 4.417209 231.2973 at 10iterations 2.107482 88.17934 at 20iterations 0.9999077 35.19522 at 30iterations 0.4788864 14.78726 at 40iterations 0.2280090 7.128540 at 50iterations 0.1089572 3.684827 at 60iterations 5.2141689E-02 1.636932 at 70iterations 2.4868747E-02 0.7388127 at 80iterations 1.1889520E-02 0.3763771 at 90iterations 5.6956513E-03 0.1836088 at 100iterations 2.7549251E-03 9.9990845E-02 at 110iterations 1.3488468E-03 4.2526245E-02 at 120iterations finished qdiffx linear iterations at : 14:39:34 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 1.3488468E-03 4.2526245E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 14:39:35 7.197u 0.220s 0:08.27 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 Mon Oct 10 2011 at 14:39:35 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 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: 2.949841 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 2.949841 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.9852 centred at (gu) : 91.30353 86.97449 91.28925 assigned negative charge : -362.4858 centred at (gu) : 90.46306 87.04724 91.60188 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 171125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20972 grid for indexing accessible points = 1.400000 m= 87595 mr = 123870 m= 34040 mr = 71698 m= 9136 mr = 27306 m= 1544 mr = 6859 m= 113 mr = 1030 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 72758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 17844 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) : 1.966561 object centre at (A) : 44.68700 49.58200 53.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3790185 -0.2278286 midg,1,midg; midg,igrid,midg 6.6120073E-02 -6.2254094E-02 1,midg,midg; igrid,midg,midg -1.5934345E-03 0.3402473 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.660000 now iterating at: 14:39:37 rms-change max change #iterations 10.18268 360.9128 at 10iterations 5.988046 140.7471 at 20iterations 3.507264 77.03986 at 30iterations 2.047361 43.07598 at 40iterations 1.192424 23.28030 at 50iterations 0.6932617 12.72686 at 60iterations 0.4022516 7.565432 at 70iterations 0.2333944 4.218542 at 80iterations 0.1353444 3.094258 at 90iterations 7.8228295E-02 1.495723 at 100iterations 4.5266069E-02 0.7612038 at 110iterations 2.6206035E-02 0.5156479 at 120iterations 1.5134396E-02 0.3150663 at 130iterations 8.7477528E-03 0.1648140 at 140iterations 5.0776638E-03 9.0996742E-02 at 150iterations 2.9423996E-03 5.7792664E-02 at 160iterations 1.7180914E-03 3.1372070E-02 at 170iterations 1.0135683E-03 1.8870354E-02 at 180iterations finished qdiffx linear iterations at : 14:39:47 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 1.0135683E-03 1.8870354E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 14:39:48 12.082u 0.225s 0:12.80 96.0% 0+0k 0+0io 0pf+0w