Mon Oct 10 01:21:23 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 Mon Oct 10 2011 at 01:21:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6289641 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 0.6289641 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.77022 92.54752 89.94709 assigned negative charge : -286.4003 centred at (gu) : 90.86827 92.67913 89.89291 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5414 nv = 96 ne = 84 npr = 39772 no. pairs analyzed = 39772 no. exposed pairs = 2490 no. arc points = 17430 no. surface atoms = 850 nbur = 1120 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3027 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1771 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5460067E-11 6.7476038E-09 midg,1,midg; midg,igrid,midg 6.7023698E-09 -8.9602690E-09 1,midg,midg; igrid,midg,midg 8.0697093E-09 -3.3415801E-09 gauss-seidel spectral radius is 0.9868534 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 01:21:24 rms-change max change #iterations 0.1141192 20.89691 at 10iterations 1.0751610E-02 1.947018 at 20iterations 1.0324903E-03 0.1698008 at 30iterations 9.6277086E-05 1.6349792E-02 at 40iterations 9.1883248E-06 1.4533997E-03 at 50iterations finished qdiffx linear iterations at : 01:21:26 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 9.1883248E-06 1.4533997E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 01:21:27 3.285u 0.152s 0:03.74 91.7% 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 01:21:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.886892 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 1.886892 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 92.31065 97.64259 89.84113 assigned negative charge : -286.4003 centred at (gu) : 92.60508 98.03767 89.67880 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 57811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 22050 mr = 39790 m= 3484 mr = 16964 m= 173 mr = 2313 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2441 time to turn everything in is 0.4700000 number of dielectric boundary points 24376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14420 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) : 0.6289641 object centre at (A) : 14.59500 22.45300 3.827501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6459515E-02 1.9471103E-02 midg,1,midg; midg,igrid,midg 2.5915360E-02 -8.5711917E-03 1,midg,midg; igrid,midg,midg 6.8485797E-03 -4.7414461E-03 gauss-seidel spectral radius is 0.9985338 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 01:21:28 rms-change max change #iterations 3.505008 163.7890 at 10iterations 1.590591 73.83861 at 20iterations 0.7261882 30.23997 at 30iterations 0.3314483 11.47172 at 40iterations 0.1504445 5.182585 at 50iterations 6.8817146E-02 2.682288 at 60iterations 3.1308424E-02 1.169831 at 70iterations 1.4237648E-02 0.5413599 at 80iterations 6.4853462E-03 0.2225876 at 90iterations 2.9687269E-03 0.1296539 at 100iterations 1.3431014E-03 4.6165466E-02 at 110iterations 6.1335339E-04 2.3727417E-02 at 120iterations finished qdiffx linear iterations at : 01:21:35 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 6.1335339E-04 2.3727417E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 01:21:35 7.996u 0.246s 0:08.51 96.7% 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 01:21:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.830339 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 2.830339 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 93.46587 101.4639 89.76169 assigned negative charge : -286.4003 centred at (gu) : 93.90771 102.0565 89.51826 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 133267 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 69999 mr = 95996 m= 26888 mr = 58450 m= 6298 mr = 22515 m= 807 mr = 4889 m= 33 mr = 564 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 7814 time to turn everything in is 1.160000 number of dielectric boundary points 54862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 14702 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) : 1.886892 object centre at (A) : 14.59500 22.45300 3.827501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.070869 8.7642141E-02 midg,1,midg; midg,igrid,midg 0.2736623 -0.1158871 1,midg,midg; igrid,midg,midg 4.4641174E-02 -3.4503166E-02 gauss-seidel spectral radius is 0.9992162 estimated iterations to convergence 282 setup time was (sec) 1.490000 now iterating at: 01:21:37 rms-change max change #iterations 8.355956 387.6232 at 10iterations 4.788298 137.4352 at 20iterations 2.726335 65.98291 at 30iterations 1.549749 36.82240 at 40iterations 0.8775513 18.48518 at 50iterations 0.4975229 11.08014 at 60iterations 0.2813210 5.835697 at 70iterations 0.1590327 3.265030 at 80iterations 8.9788243E-02 1.891332 at 90iterations 5.0890643E-02 1.063736 at 100iterations 2.8704446E-02 0.6530905 at 110iterations 1.6186099E-02 0.3310370 at 120iterations 9.1548469E-03 0.1785793 at 130iterations 5.1655262E-03 0.1073074 at 140iterations 2.9132464E-03 5.6693316E-02 at 150iterations 1.6459849E-03 3.3808708E-02 at 160iterations 9.2752284E-04 1.8696785E-02 at 170iterations 5.2399328E-04 1.0168076E-02 at 180iterations finished qdiffx linear iterations at : 01:21:48 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 5.2399328E-04 1.0168076E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 01:21:49 12.755u 0.275s 0:13.36 97.4% 0+0k 0+0io 0pf+0w