Mon Oct 10 16:03:06 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 16:03:06 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 has a net charge of 1.4000 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: 0.5394920 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 0.5394920 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4593 net assigned charge : 3.012007 assigned positive charge : 717.6985 centred at (gu) : 90.28394 90.94447 89.55133 assigned negative charge : -714.6910 centred at (gu) : 90.21230 90.94809 89.56309 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8873 nv = 96 ne = 84 npr = 97300 no. pairs analyzed = 97300 no. exposed pairs = 5770 no. arc points = 39109 no. surface atoms = 1936 nbur = 2824 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 353 mr = 4875 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 4327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3982 ## 538 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6931657E-10 4.0427935E-11 midg,1,midg; midg,igrid,midg 1.3752598E-10 1.4145217E-10 1,midg,midg; igrid,midg,midg -4.2837547E-10 7.9052437E-10 gauss-seidel spectral radius is 0.9824187 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 16:03:07 rms-change max change #iterations 9.1020733E-02 14.22056 at 10iterations 6.1666584E-03 1.043388 at 20iterations 7.3338766E-04 0.1361389 at 30iterations 2.3714631E-04 4.0752411E-02 at 40iterations 9.5592914E-05 1.3795853E-02 at 50iterations finished qdiffx linear iterations at : 16:03:10 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 9.5592914E-05 1.3795853E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:03:10 3.488u 0.171s 0:03.94 92.6% 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 16:03:10 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 has a net charge of 1.4000 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: 1.618476 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 1.618476 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4593 net assigned charge : 3.012007 assigned positive charge : 717.6985 centred at (gu) : 90.84997 92.83218 88.65242 assigned negative charge : -714.6910 centred at (gu) : 90.63634 92.84391 88.68838 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31790 mr = 70782 m= 3411 mr = 22349 m= 92 mr = 1716 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.4700000 number of dielectric boundary points 40307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 416 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 35022 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) : 0.5394920 object centre at (A) : 12.99900 40.19700 64.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8508641E-03 1.0556365E-02 midg,1,midg; midg,igrid,midg -5.2054101E-03 -1.4949528E-02 1,midg,midg; igrid,midg,midg -3.0507555E-02 2.1482978E-02 gauss-seidel spectral radius is 0.9983274 estimated iterations to convergence 194 setup time was (sec) 0.6800000 now iterating at: 16:03:11 rms-change max change #iterations 4.307587 166.1893 at 10iterations 1.859539 64.19894 at 20iterations 0.8020233 23.00927 at 30iterations 0.3472718 10.54822 at 40iterations 0.1498067 4.537103 at 50iterations 6.4868644E-02 1.854459 at 60iterations 2.8130203E-02 0.8234005 at 70iterations 1.2264044E-02 0.3669319 at 80iterations 5.3651812E-03 0.1626678 at 90iterations 2.3936748E-03 7.5042725E-02 at 100iterations 1.1190122E-03 3.6634445E-02 at 110iterations 5.7505735E-04 1.7990112E-02 at 120iterations finished qdiffx linear iterations at : 16:03:18 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 5.7505735E-04 1.7990112E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 16:03:19 7.908u 0.201s 0:08.53 94.9% 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 Mon Oct 10 2011 at 16:03:19 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 has a net charge of 1.4000 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: 2.427714 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 2.427714 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4593 net assigned charge : 3.012007 assigned positive charge : 717.6985 centred at (gu) : 91.27465 94.24771 87.97824 assigned negative charge : -714.6910 centred at (gu) : 90.95447 94.26564 88.03255 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 232629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110709 mr = 173567 m= 32142 mr = 88433 m= 5262 mr = 24398 m= 359 mr = 3474 m= 2 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1936 time to turn everything in is 1.190000 number of dielectric boundary points 91064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 36696 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) : 1.618476 object centre at (A) : 12.99900 40.19700 64.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3656756E-02 0.1539210 midg,1,midg; midg,igrid,midg -0.1370784 -0.3222614 1,midg,midg; igrid,midg,midg -0.5527702 0.2813790 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.430000 now iterating at: 16:03:20 rms-change max change #iterations 11.17225 300.9456 at 10iterations 6.522294 141.7612 at 20iterations 3.779253 76.98221 at 30iterations 2.188269 47.60958 at 40iterations 1.259621 23.53802 at 50iterations 0.7241753 14.14799 at 60iterations 0.4139712 8.193680 at 70iterations 0.2364707 4.336557 at 80iterations 0.1353273 2.502785 at 90iterations 7.7143200E-02 1.330297 at 100iterations 4.4033024E-02 0.7392960 at 110iterations 2.5126785E-02 0.4117414 at 120iterations 1.4307194E-02 0.2585373 at 130iterations 8.1800250E-03 0.1340275 at 140iterations 4.6975063E-03 8.5947037E-02 at 150iterations 2.7258361E-03 4.8299313E-02 at 160iterations 1.6133302E-03 2.7430534E-02 at 170iterations 9.8857493E-04 1.6418457E-02 at 180iterations finished qdiffx linear iterations at : 16:03:32 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 9.8857493E-04 1.6418457E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 16:03:32 13.169u 0.215s 0:13.65 97.9% 0+0k 0+0io 0pf+0w