Mon Oct 10 14:39:08 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 14:39:08 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 0.6051334 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 0.6051334 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 367.3321 centred at (gu) : 90.16455 89.44260 89.24491 assigned negative charge : -371.3324 centred at (gu) : 89.94115 89.48904 89.27635 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 49876 no. pairs analyzed = 49876 no. exposed pairs = 3365 no. arc points = 23600 no. surface atoms = 1136 nbur = 1357 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3133 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9370650E-10 -2.8249627E-09 midg,1,midg; midg,igrid,midg -1.6827899E-10 -3.4953536E-09 1,midg,midg; igrid,midg,midg -1.0998932E-08 7.1192279E-09 gauss-seidel spectral radius is 0.9858629 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 14:39:09 rms-change max change #iterations 0.1115253 18.77711 at 10iterations 9.7568911E-03 1.792191 at 20iterations 8.2061003E-04 0.1288319 at 30iterations 7.2156188E-05 1.3051510E-02 at 40iterations 6.2271774E-06 1.0480881E-03 at 50iterations finished qdiffx linear iterations at : 14:39:12 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 6.2271774E-06 1.0480881E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 14:39:13 4.499u 0.420s 0:05.26 93.3% 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 Mon Oct 10 2011 at 14:39:13 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 1.815400 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 1.815400 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 367.3321 centred at (gu) : 90.49308 88.32714 87.73425 assigned negative charge : -371.3324 centred at (gu) : 89.82331 88.46667 87.82872 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 67275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 22279 mr = 44976 m= 2841 mr = 15465 m= 123 mr = 1370 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 30681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 18231 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) : 0.6051334 object centre at (A) : 18.17750 31.33500 12.45450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0836671E-03 -1.1350629E-02 midg,1,midg; midg,igrid,midg -1.2134715E-02 2.2413277E-03 1,midg,midg; igrid,midg,midg -3.6194418E-02 5.8585326E-03 gauss-seidel spectral radius is 0.9984953 estimated iterations to convergence 204 setup time was (sec) 1.040000 now iterating at: 14:39:14 rms-change max change #iterations 3.770314 186.1157 at 10iterations 1.682494 59.99245 at 20iterations 0.7626524 27.12960 at 30iterations 0.3420891 11.80460 at 40iterations 0.1540066 5.069046 at 50iterations 6.9787040E-02 2.514091 at 60iterations 3.1225629E-02 1.163389 at 70iterations 1.4096925E-02 0.5034475 at 80iterations 6.3571306E-03 0.2181473 at 90iterations 2.8705436E-03 0.1034721 at 100iterations 1.2874517E-03 4.3592453E-02 at 110iterations 5.8193441E-04 2.1471024E-02 at 120iterations finished qdiffx linear iterations at : 14:39:24 total time elapsed so far: 10.62000 # loops : 120 mean,max change (kT/e) : 5.8193441E-04 2.1471024E-02 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 14:39:25 10.844u 0.479s 0:12.06 93.7% 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 14:39:25 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 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: 2.723100 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 2.723100 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 367.3321 centred at (gu) : 90.73956 87.49052 86.60116 assigned negative charge : -371.3324 centred at (gu) : 89.73478 87.69991 86.74290 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 155746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 74781 mr = 109911 m= 23818 mr = 59204 m= 4595 mr = 17823 m= 472 mr = 2997 m= 46 mr = 245 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 69257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 18671 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) : 1.815400 object centre at (A) : 18.17750 31.33500 12.45450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1800206E-02 -0.1776866 midg,1,midg; midg,igrid,midg -0.1686533 8.0879904E-02 1,midg,midg; igrid,midg,midg -0.4074246 3.1772479E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 2.180000 now iterating at: 14:39:28 rms-change max change #iterations 9.166523 270.7283 at 10iterations 5.354327 134.9261 at 20iterations 3.088828 95.92466 at 30iterations 1.775109 38.63838 at 40iterations 1.019896 24.88487 at 50iterations 0.5818412 12.32225 at 60iterations 0.3323313 7.098202 at 70iterations 0.1895214 4.106880 at 80iterations 0.1077942 2.288417 at 90iterations 6.1340887E-02 1.319992 at 100iterations 3.4899976E-02 0.7504578 at 110iterations 1.9792857E-02 0.3816719 at 120iterations 1.1221902E-02 0.2078590 at 130iterations 6.3763768E-03 0.1298769 at 140iterations 3.6153414E-03 8.0415249E-02 at 150iterations 2.0457143E-03 4.2747498E-02 at 160iterations 1.1616230E-03 2.8020859E-02 at 170iterations 6.5734988E-04 1.3154984E-02 at 180iterations finished qdiffx linear iterations at : 14:39:47 total time elapsed so far: 21.27000 # loops : 180 mean,max change (kT/e) : 6.5734988E-04 1.3154984E-02 energy calculations done at 21.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.50000 DelPhi exited at 14:39:48 21.503u 0.498s 0:22.64 97.1% 0+0k 0+0io 0pf+0w