Sat Oct 15 12:34:19 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 Sat Oct 15 2011 at 12:34:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7027518 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): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 0.7027518 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 89.89902 90.75721 90.84153 assigned negative charge : -327.3089 centred at (gu) : 89.80113 90.85747 90.96597 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7350 nv = 96 ne = 84 npr = 45987 no. pairs analyzed = 45987 no. exposed pairs = 2660 no. arc points = 19136 no. surface atoms = 904 nbur = 1316 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 502 mr = 4102 m= 7 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.1700000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1817 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8341 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7967841E-08 -1.5285311E-08 midg,1,midg; midg,igrid,midg 7.9940399E-08 -1.5321542E-09 1,midg,midg; igrid,midg,midg 1.7267672E-10 8.9738172E-08 gauss-seidel spectral radius is 0.9894643 estimated iterations to convergence 79 setup time was (sec) 0.4000000 now iterating at: 12:34:20 rms-change max change #iterations 0.2026203 30.61960 at 10iterations 2.4439752E-02 3.161282 at 20iterations 2.9374440E-03 0.3744354 at 30iterations 3.5863792E-04 4.9858093E-02 at 40iterations 4.3693337E-05 5.5084229E-03 at 50iterations finished qdiffx linear iterations at : 12:34:23 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 4.3693337E-05 5.5084229E-03 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 12:34:23 3.785u 0.211s 0:04.40 90.6% 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 Sat Oct 15 2011 at 12:34:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.108255 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): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 2.108255 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 89.69704 92.27116 92.52433 assigned negative charge : -327.3089 centred at (gu) : 89.40334 92.57246 92.89798 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19136 grid for indexing accessible points = 1.400000 m= 30356 mr = 54192 m= 6202 mr = 23021 m= 613 mr = 4292 m= 26 mr = 302 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4144 time to turn everything in is 0.4100000 number of dielectric boundary points 33543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16575 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) : 0.7027518 object centre at (A) : 7.216000 5.116000 15.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1381400E-02 2.4980966E-02 midg,1,midg; midg,igrid,midg 3.7403587E-02 9.2351027E-03 1,midg,midg; igrid,midg,midg -1.0883043E-02 3.6029585E-02 gauss-seidel spectral radius is 0.9988346 estimated iterations to convergence 232 setup time was (sec) 0.6500000 now iterating at: 12:34:24 rms-change max change #iterations 4.762117 238.2279 at 10iterations 2.344692 91.11871 at 20iterations 1.162715 34.31271 at 30iterations 0.5775034 17.90404 at 40iterations 0.2863299 8.635101 at 50iterations 0.1423573 4.493776 at 60iterations 7.0712909E-02 2.037493 at 70iterations 3.4870837E-02 1.104338 at 80iterations 1.7308852E-02 0.4890695 at 90iterations 8.5615460E-03 0.2405171 at 100iterations 4.2561041E-03 0.1238966 at 110iterations 2.1127055E-03 6.2362671E-02 at 120iterations finished qdiffx linear iterations at : 12:34:32 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 2.1127055E-03 6.2362671E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 12:34:32 8.526u 0.237s 0:09.02 97.0% 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 Sat Oct 15 2011 at 12:34:32 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 = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.162383 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): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 3.162383 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 89.54538 93.40651 93.78658 assigned negative charge : -327.3089 centred at (gu) : 89.10500 93.85864 94.34697 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19136 grid for indexing accessible points = 1.400000 m= 94471 mr = 130476 m= 38723 mr = 78508 m= 11937 mr = 31952 m= 2456 mr = 9429 m= 313 mr = 1831 m= 20 mr = 192 m= 0 mr = 8 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 14598 time to turn everything in is 1.240000 number of dielectric boundary points 75652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 16664 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) : 2.108255 object centre at (A) : 7.216000 5.116000 15.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5658578 0.2481744 midg,1,midg; midg,igrid,midg 0.3148171 0.2362640 1,midg,midg; igrid,midg,midg -3.2657951E-02 0.2538882 gauss-seidel spectral radius is 0.9992895 estimated iterations to convergence 296 setup time was (sec) 1.520000 now iterating at: 12:34:34 rms-change max change #iterations 10.35487 464.8469 at 10iterations 6.009177 124.0627 at 20iterations 3.480342 65.76267 at 30iterations 2.019687 34.18690 at 40iterations 1.173764 20.03996 at 50iterations 0.6790749 11.31205 at 60iterations 0.3941556 7.488867 at 70iterations 0.2288346 4.015587 at 80iterations 0.1324452 2.272047 at 90iterations 7.7070512E-02 1.343893 at 100iterations 4.4570964E-02 0.7884102 at 110iterations 2.5895327E-02 0.4158173 at 120iterations 1.5024202E-02 0.2616291 at 130iterations 8.7308716E-03 0.1469650 at 140iterations 5.0536157E-03 9.8932266E-02 at 150iterations 2.9283848E-03 4.9766541E-02 at 160iterations 1.7019120E-03 2.9833794E-02 at 170iterations 9.8659494E-04 1.6281128E-02 at 180iterations finished qdiffx linear iterations at : 12:34:48 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 9.8659494E-04 1.6281128E-02 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 12:34:48 14.915u 0.286s 0:15.60 97.3% 0+0k 0+0io 0pf+0w