Wed Feb 15 08:54:56 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:57 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 = 2005 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 193 has a net charge of -3.0000 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: 0.6673540 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): -1.036000 45.43400 ymin,ymax (A): -13.69800 36.01900 zmin,zma (A): -29.67900 23.66600 x,y,z range (A): 46.47000 49.71700 53.34500 scale (grids/A): 0.6673540 object centre (A): 22.19900 11.16050 -3.006499 number of atom coordinates read : 2005 total number of charged atoms : 1866 net assigned charge : -2.499985 assigned positive charge : 301.1460 centred at (gu) : 88.37016 89.90445 91.34678 assigned negative charge : -303.6461 centred at (gu) : 88.59822 89.93787 91.39183 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5832 nv = 96 ne = 84 npr = 43556 no. pairs analyzed = 43556 no. exposed pairs = 2504 no. arc points = 17688 no. surface atoms = 847 nbur = 1158 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3124 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2800000 number of dielectric boundary points 2975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0011059E-11 -2.2072273E-08 midg,1,midg; midg,igrid,midg -2.1489814E-09 -1.4251115E-08 1,midg,midg; igrid,midg,midg 4.6940343E-08 -3.6916184E-08 gauss-seidel spectral radius is 0.9883036 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 08:54:57 rms-change max change #iterations 0.1521844 25.23311 at 10iterations 1.6873620E-02 2.373662 at 20iterations 1.7764088E-03 0.2681427 at 30iterations 1.9302212E-04 2.8070450E-02 at 40iterations 2.1027787E-05 4.0674210E-03 at 50iterations finished qdiffx linear iterations at : 08:55:00 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.1027787E-05 4.0674210E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:55:01 3.357u 0.160s 0:03.84 91.4% 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 Wed Feb 15 2012 at 08:55:01 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 = 2005 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 193 has a net charge of -3.0000 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: 2.002062 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): -1.036000 45.43400 ymin,ymax (A): -13.69800 36.01900 zmin,zma (A): -29.67900 23.66600 x,y,z range (A): 46.47000 49.71700 53.34500 scale (grids/A): 2.002062 object centre (A): 22.19900 11.16050 -3.006499 number of atom coordinates read : 2005 total number of charged atoms : 1866 net assigned charge : -2.499985 assigned positive charge : 301.1460 centred at (gu) : 85.11050 89.71303 94.04037 assigned negative charge : -303.6461 centred at (gu) : 85.79479 89.81358 94.17551 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17688 grid for indexing accessible points = 1.400000 m= 21991 mr = 42776 m= 3601 mr = 16113 m= 241 mr = 2188 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2201 time to turn everything in is 0.5300000 number of dielectric boundary points 27486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14761 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) : 0.6673540 object centre at (A) : 22.19900 11.16050 -3.006499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5031516E-02 -5.0978046E-02 midg,1,midg; midg,igrid,midg -3.4472197E-02 -1.5261507E-02 1,midg,midg; igrid,midg,midg 5.1904239E-02 -3.0414142E-02 gauss-seidel spectral radius is 0.9986944 estimated iterations to convergence 219 setup time was (sec) 0.8000000 now iterating at: 08:55:02 rms-change max change #iterations 4.101992 175.8637 at 10iterations 1.949632 89.74619 at 20iterations 0.9276096 33.30445 at 30iterations 0.4405274 14.27437 at 40iterations 0.2091279 8.797959 at 50iterations 0.1001419 3.445274 at 60iterations 4.7475733E-02 1.562079 at 70iterations 2.2604330E-02 0.7199860 at 80iterations 1.0759750E-02 0.3694859 at 90iterations 5.1118825E-03 0.1733365 at 100iterations 2.4358248E-03 7.5736046E-02 at 110iterations 1.1587427E-03 4.3254852E-02 at 120iterations finished qdiffx linear iterations at : 08:55:08 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 1.1587427E-03 4.3254852E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 08:55:09 7.459u 0.179s 0:07.94 95.9% 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 Wed Feb 15 2012 at 08:55:09 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 = 2005 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 193 has a net charge of -3.0000 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: 3.003093 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): -1.036000 45.43400 ymin,ymax (A): -13.69800 36.01900 zmin,zma (A): -29.67900 23.66600 x,y,z range (A): 46.47000 49.71700 53.34500 scale (grids/A): 3.003093 object centre (A): 22.19900 11.16050 -3.006499 number of atom coordinates read : 2005 total number of charged atoms : 1866 net assigned charge : -2.499985 assigned positive charge : 301.1460 centred at (gu) : 82.66570 89.56939 96.06053 assigned negative charge : -303.6461 centred at (gu) : 83.69218 89.72037 96.26334 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 145332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17688 grid for indexing accessible points = 1.400000 m= 71023 mr = 103732 m= 25627 mr = 57832 m= 6364 mr = 20440 m= 966 mr = 4718 m= 73 mr = 624 m= 0 mr = 30 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 7320 time to turn everything in is 1.310000 number of dielectric boundary points 62009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 14928 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) : 2.002062 object centre at (A) : 22.19900 11.16050 -3.006499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5536659 -0.7429398 midg,1,midg; midg,igrid,midg -0.5182343 -0.2266715 1,midg,midg; igrid,midg,midg 0.6229334 -0.2637454 gauss-seidel spectral radius is 0.9992624 estimated iterations to convergence 291 setup time was (sec) 1.640000 now iterating at: 08:55:11 rms-change max change #iterations 9.424549 408.0094 at 10iterations 5.424073 121.4280 at 20iterations 3.130621 70.26254 at 30iterations 1.799591 38.54767 at 40iterations 1.036941 20.49067 at 50iterations 0.5954082 12.62233 at 60iterations 0.3422137 6.436653 at 70iterations 0.1965694 4.366956 at 80iterations 0.1128361 2.215787 at 90iterations 6.4820863E-02 1.247072 at 100iterations 3.7150782E-02 0.7389441 at 110iterations 2.1334259E-02 0.4010882 at 120iterations 1.2246077E-02 0.2514944 at 130iterations 7.0305192E-03 0.1375380 at 140iterations 4.0321848E-03 7.8543186E-02 at 150iterations 2.3156789E-03 4.3365479E-02 at 160iterations 1.3267136E-03 3.0622482E-02 at 170iterations 7.6421711E-04 1.4643669E-02 at 180iterations finished qdiffx linear iterations at : 08:55:21 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 7.6421711E-04 1.4643669E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 08:55:22 12.516u 0.319s 0:13.31 96.3% 0+0k 0+0io 0pf+0w