Sun Oct 9 06:53:49 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 Sun Oct 9 2011 at 06:53:49 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: 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 0.1500000 boundary points on vw surface= 5897 nv = 96 ne = 84 npr = 42642 no. pairs analyzed = 42642 no. exposed pairs = 2488 no. arc points = 17532 no. surface atoms = 840 nbur = 1165 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3209 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2600000 number of dielectric boundary points 2953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1675 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3600000 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 0.9883042 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 06:53:49 rms-change max change #iterations 0.1522781 25.23445 at 10iterations 1.6929319E-02 2.296736 at 20iterations 1.7882525E-03 0.2545853 at 30iterations 1.9429426E-04 2.7538300E-02 at 40iterations 2.0999501E-05 3.6354065E-03 at 50iterations finished qdiffx linear iterations at : 06:53:52 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.0999501E-05 3.6354065E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 06:53:52 3.055u 0.133s 0:03.48 91.3% 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 Sun Oct 9 2011 at 06:53:52 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: 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 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 63641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17532 grid for indexing accessible points = 1.400000 m= 22449 mr = 43738 m= 3728 mr = 16617 m= 267 mr = 2330 m= 4 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2605 time to turn everything in is 0.4500000 number of dielectric boundary points 27284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.5600000 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 2.5050750E-02 -5.1105957E-02 midg,1,midg; midg,igrid,midg -3.4175847E-02 -1.5190911E-02 1,midg,midg; igrid,midg,midg 5.2799281E-02 -3.0427054E-02 gauss-seidel spectral radius is 0.9986946 estimated iterations to convergence 219 setup time was (sec) 0.7100000 now iterating at: 06:53:53 rms-change max change #iterations 4.104856 175.8748 at 10iterations 1.953228 90.74341 at 20iterations 0.9290289 34.20244 at 30iterations 0.4409886 15.20198 at 40iterations 0.2098149 8.280417 at 50iterations 0.1003173 3.174990 at 60iterations 4.7632210E-02 1.596119 at 70iterations 2.2681516E-02 0.7570944 at 80iterations 1.0807268E-02 0.3494873 at 90iterations 5.1295403E-03 0.1851397 at 100iterations 2.4443336E-03 8.2481384E-02 at 110iterations 1.1648881E-03 4.0073395E-02 at 120iterations finished qdiffx linear iterations at : 06:53:59 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 1.1648881E-03 4.0073395E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 06:54:00 6.855u 0.165s 0:07.30 96.0% 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 Sun Oct 9 2011 at 06:54:00 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 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 147261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17532 grid for indexing accessible points = 1.400000 m= 72702 mr = 106002 m= 26276 mr = 59549 m= 6649 mr = 21093 m= 1082 mr = 5045 m= 101 mr = 742 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 8930 time to turn everything in is 1.110000 number of dielectric boundary points 61585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 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 0.5538315 -0.7436510 midg,1,midg; midg,igrid,midg -0.5193565 -0.2259327 1,midg,midg; igrid,midg,midg 0.6327591 -0.2638864 gauss-seidel spectral radius is 0.9992618 estimated iterations to convergence 290 setup time was (sec) 1.380000 now iterating at: 06:54:01 rms-change max change #iterations 9.415350 407.9226 at 10iterations 5.413517 117.2458 at 20iterations 3.122304 70.21232 at 30iterations 1.793214 38.51427 at 40iterations 1.034281 20.56634 at 50iterations 0.5937558 12.61582 at 60iterations 0.3413254 6.290321 at 70iterations 0.1958969 4.483610 at 80iterations 0.1124869 2.183943 at 90iterations 6.4575180E-02 1.289465 at 100iterations 3.6989946E-02 0.6714954 at 110iterations 2.1231212E-02 0.3891563 at 120iterations 1.2198790E-02 0.2625904 at 130iterations 6.9975154E-03 0.1393929 at 140iterations 4.0179915E-03 7.2855115E-02 at 150iterations 2.3051647E-03 4.5886040E-02 at 160iterations 1.3215478E-03 2.7324677E-02 at 170iterations 7.6093839E-04 1.4190674E-02 at 180iterations finished qdiffx linear iterations at : 06:54:11 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 7.6093839E-04 1.4190674E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 06:54:11 11.064u 0.213s 0:11.57 97.4% 0+0k 0+0io 0pf+0w