Sat Oct 8 11:36:33 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 8 2011 at 11:36:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3357 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: ZN4 476 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6329226 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): -8.125000 42.77000 ymin,ymax (A): -14.23000 42.01700 zmin,zma (A): -2.878000 46.49500 x,y,z range (A): 50.89500 56.24700 49.37300 scale (grids/A): 0.6329226 object centre (A): 17.32250 13.89350 21.80850 number of atom coordinates read : 3357 total number of charged atoms : 3205 net assigned charge : -4.999964 assigned positive charge : 511.8683 centred at (gu) : 90.41624 89.48799 91.06800 assigned negative charge : -516.8693 centred at (gu) : 90.23927 89.57907 91.06927 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8599 nv = 96 ne = 84 npr = 72243 no. pairs analyzed = 72243 no. exposed pairs = 3632 no. arc points = 24651 no. surface atoms = 1222 nbur = 2135 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 5217 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 0.4200000 number of dielectric boundary points 3752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2465 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7282942E-09 -7.7958582E-09 midg,1,midg; midg,igrid,midg 6.1471468E-09 -1.5948252E-08 1,midg,midg; igrid,midg,midg -2.6589611E-08 1.7686066E-08 gauss-seidel spectral radius is 0.9871182 estimated iterations to convergence 72 setup time was (sec) 0.7000000 now iterating at: 11:36:34 rms-change max change #iterations 0.1659700 21.48959 at 10iterations 1.6130112E-02 2.082279 at 20iterations 1.5791588E-03 0.1984940 at 30iterations 1.5430505E-04 1.8848419E-02 at 40iterations 1.4958343E-05 1.7547607E-03 at 50iterations finished qdiffx linear iterations at : 11:36:37 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.4958343E-05 1.7547607E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 11:36:38 4.210u 0.265s 0:04.82 92.7% 0+0k 0+0io 6pf+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 8 2011 at 11:36:38 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3357 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: ZN4 476 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.898768 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): -8.125000 42.77000 ymin,ymax (A): -14.23000 42.01700 zmin,zma (A): -2.878000 46.49500 x,y,z range (A): 50.89500 56.24700 49.37300 scale (grids/A): 1.898768 object centre (A): 17.32250 13.89350 21.80850 number of atom coordinates read : 3357 total number of charged atoms : 3205 net assigned charge : -4.999964 assigned positive charge : 511.8683 centred at (gu) : 91.24792 88.46272 93.20329 assigned negative charge : -516.8693 centred at (gu) : 90.71735 88.73643 93.20750 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 93594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24651 grid for indexing accessible points = 1.400000 m= 35018 mr = 68621 m= 5710 mr = 27402 m= 322 mr = 3872 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 8191 time to turn everything in is 0.8200000 number of dielectric boundary points 34636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 25209 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) : 0.6329226 object centre at (A) : 17.32250 13.89350 21.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7786389E-02 -2.9581115E-02 midg,1,midg; midg,igrid,midg -1.9154635E-03 -5.3165380E-02 1,midg,midg; igrid,midg,midg -4.7170982E-02 1.3940210E-03 gauss-seidel spectral radius is 0.9986793 estimated iterations to convergence 218 setup time was (sec) 1.130000 now iterating at: 11:36:39 rms-change max change #iterations 4.986282 179.2114 at 10iterations 2.357719 72.15607 at 20iterations 1.122193 37.01712 at 30iterations 0.5343791 14.00574 at 40iterations 0.2525108 7.484291 at 50iterations 0.1202229 3.315462 at 60iterations 5.7116881E-02 1.700792 at 70iterations 2.7133361E-02 0.8023453 at 80iterations 1.2897723E-02 0.4133377 at 90iterations 6.1337342E-03 0.1746368 at 100iterations 2.9234658E-03 7.5236320E-02 at 110iterations 1.3884206E-03 3.6451221E-02 at 120iterations finished qdiffx linear iterations at : 11:36:48 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 1.3884206E-03 3.6451221E-02 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 11:36:49 9.930u 0.317s 0:10.55 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 8 2011 at 11:36:49 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3357 !!! WARNING: HIZ 12 has a net charge of 0.2000 !!! WARNING: HIZ 14 has a net charge of 0.2000 !!! WARNING: HIZ 211 has a net charge of 0.2000 !!! WARNING: ZN4 476 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.848152 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): -8.125000 42.77000 ymin,ymax (A): -14.23000 42.01700 zmin,zma (A): -2.878000 46.49500 x,y,z range (A): 50.89500 56.24700 49.37300 scale (grids/A): 2.848152 object centre (A): 17.32250 13.89350 21.80850 number of atom coordinates read : 3357 total number of charged atoms : 3205 net assigned charge : -4.999964 assigned positive charge : 511.8683 centred at (gu) : 91.87146 87.69404 94.80473 assigned negative charge : -516.8693 centred at (gu) : 91.07595 88.10435 94.81116 start vw surface at 0.1800000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 217195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24651 grid for indexing accessible points = 1.400000 m= 113314 mr = 166016 m= 42158 mr = 95750 m= 10348 mr = 35649 m= 1496 mr = 8169 m= 88 mr = 1020 m= 0 mr = 36 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 27750 time to turn everything in is 2.100000 number of dielectric boundary points 77959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 25638 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) : 1.898768 object centre at (A) : 17.32250 13.89350 21.80850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2641344 -0.2809425 midg,1,midg; midg,igrid,midg -0.1669395 -0.6075920 1,midg,midg; igrid,midg,midg -0.4561354 -6.7341641E-02 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 2.440000 now iterating at: 11:36:51 rms-change max change #iterations 11.37877 407.0075 at 10iterations 6.616769 117.9521 at 20iterations 3.840102 64.45776 at 30iterations 2.224330 37.75770 at 40iterations 1.287712 22.47723 at 50iterations 0.7441016 11.17866 at 60iterations 0.4308762 6.503299 at 70iterations 0.2483775 4.070221 at 80iterations 0.1435623 2.112297 at 90iterations 8.3019644E-02 1.331020 at 100iterations 4.7869653E-02 0.8006306 at 110iterations 2.7641341E-02 0.4504042 at 120iterations 1.5959218E-02 0.2554016 at 130iterations 9.2242761E-03 0.1504588 at 140iterations 5.3218845E-03 8.5166931E-02 at 150iterations 3.0799527E-03 4.8234940E-02 at 160iterations 1.7762422E-03 2.8898239E-02 at 170iterations 1.0243800E-03 1.5985489E-02 at 180iterations finished qdiffx linear iterations at : 11:37:06 total time elapsed so far: 16.78000 # loops : 180 mean,max change (kT/e) : 1.0243800E-03 1.5985489E-02 energy calculations done at 16.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 11:37:06 16.959u 0.329s 0:17.58 98.2% 0+0k 0+0io 0pf+0w