Sat Oct 8 21:07:25 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 Sat Oct 8 2011 at 21:07:25 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6238062 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 0.6238062 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 88.45082 89.59061 89.61877 assigned negative charge : -390.4956 centred at (gu) : 88.34258 89.65055 89.51003 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6586 nv = 96 ne = 84 npr = 54014 no. pairs analyzed = 54014 no. exposed pairs = 2992 no. arc points = 21357 no. surface atoms = 1007 nbur = 1584 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3682 m= 0 mr = 36 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2900000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8222 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3447663E-09 1.1238451E-08 midg,1,midg; midg,igrid,midg 9.4603312E-09 -2.2741446E-10 1,midg,midg; igrid,midg,midg -5.6849427E-09 8.6983967E-09 gauss-seidel spectral radius is 0.9866863 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 21:07:26 rms-change max change #iterations 0.1356951 19.76370 at 10iterations 1.2465405E-02 1.821247 at 20iterations 1.1735974E-03 0.2020874 at 30iterations 1.0947026E-04 1.5739441E-02 at 40iterations 1.0604525E-05 1.6641617E-03 at 50iterations finished qdiffx linear iterations at : 21:07:28 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.0604525E-05 1.6641617E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 21:07:29 3.103u 0.145s 0:03.55 91.2% 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 21:07:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 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: 1.871419 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 1.871419 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 85.35181 88.77145 88.85600 assigned negative charge : -390.4956 centred at (gu) : 85.02750 88.95129 88.52979 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21357 grid for indexing accessible points = 1.400000 m= 24742 mr = 50105 m= 3452 mr = 18377 m= 164 mr = 2056 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3867 time to turn everything in is 0.5100000 number of dielectric boundary points 29432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19353 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) : 0.6238062 object centre at (A) : -6.772500 -1.038499 16.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9734990E-02 1.7145105E-02 midg,1,midg; midg,igrid,midg 1.3851458E-02 -1.2810234E-04 1,midg,midg; igrid,midg,midg -3.8709710E-03 4.0688269E-02 gauss-seidel spectral radius is 0.9985837 estimated iterations to convergence 211 setup time was (sec) 0.7600000 now iterating at: 21:07:29 rms-change max change #iterations 4.127865 209.1835 at 10iterations 1.898356 71.55241 at 20iterations 0.8759236 29.67195 at 30iterations 0.4052308 13.34294 at 40iterations 0.1874824 6.045213 at 50iterations 8.6104229E-02 3.237323 at 60iterations 3.9996877E-02 1.348154 at 70iterations 1.8482458E-02 0.6296082 at 80iterations 8.5195359E-03 0.2959423 at 90iterations 3.9335359E-03 0.1300735 at 100iterations 1.8179868E-03 5.9218407E-02 at 110iterations 8.3781924E-04 2.6342392E-02 at 120iterations finished qdiffx linear iterations at : 21:07:35 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 8.3781924E-04 2.6342392E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 21:07:36 6.847u 0.159s 0:07.28 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 Sat Oct 8 2011 at 21:07:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.807128 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 2.807128 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.9950 centred at (gu) : 83.02768 88.15704 88.28384 assigned negative charge : -390.4956 centred at (gu) : 82.54121 88.42684 87.79470 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 165780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21357 grid for indexing accessible points = 1.400000 m= 82105 mr = 121329 m= 27689 mr = 67627 m= 6082 mr = 22244 m= 733 mr = 4432 m= 29 mr = 436 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 12373 time to turn everything in is 1.190000 number of dielectric boundary points 66345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19727 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) : 1.871419 object centre at (A) : -6.772500 -1.038499 16.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1899848 0.1555770 midg,1,midg; midg,igrid,midg 0.1569407 -3.8599065E-03 1,midg,midg; igrid,midg,midg -3.6408186E-02 0.5313727 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.470000 now iterating at: 21:07:38 rms-change max change #iterations 9.620498 318.3382 at 10iterations 5.544152 137.4950 at 20iterations 3.174439 66.78533 at 30iterations 1.810885 39.28680 at 40iterations 1.033372 22.63302 at 50iterations 0.5896322 12.57347 at 60iterations 0.3368419 7.124546 at 70iterations 0.1921549 3.404795 at 80iterations 0.1094225 2.106187 at 90iterations 6.2422499E-02 1.242325 at 100iterations 3.5528183E-02 0.7188568 at 110iterations 2.0232050E-02 0.3546715 at 120iterations 1.1537315E-02 0.2245774 at 130iterations 6.5693888E-03 0.1213694 at 140iterations 3.7486001E-03 6.6781998E-02 at 150iterations 2.1337168E-03 4.0269852E-02 at 160iterations 1.2141195E-03 2.3685455E-02 at 170iterations 6.9265417E-04 1.3215542E-02 at 180iterations finished qdiffx linear iterations at : 21:07:47 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 6.9265417E-04 1.3215542E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 21:07:47 11.068u 0.205s 0:11.55 97.4% 0+0k 0+0io 0pf+0w