Sun Oct 9 20:00:52 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 Sun Oct 9 2011 at 20:00:52 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5464 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2100000 grid size : 179 scale,in grids/A, set to be: 0.5419559 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 0.5419559 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.754056 assigned positive charge : 841.7791 centred at (gu) : 88.10172 89.20186 89.45177 assigned negative charge : -839.0311 centred at (gu) : 88.00938 89.19285 89.41071 start vw surface at 0.2900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 10119 nv = 96 ne = 84 npr = 113639 no. pairs analyzed = 113639 no. exposed pairs = 6052 no. arc points = 41425 no. surface atoms = 2068 nbur = 3396 mkacc time = 0.2600000 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= 365 mr = 5794 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4289 ## 535 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1332217E-10 5.3022930E-10 midg,1,midg; midg,igrid,midg 8.8870279E-11 2.1939048E-10 1,midg,midg; igrid,midg,midg -1.3571394E-09 7.1573591E-10 gauss-seidel spectral radius is 0.9826195 estimated iterations to convergence 62 setup time was (sec) 0.8600000 now iterating at: 20:00:53 rms-change max change #iterations 0.1057923 18.33513 at 10iterations 1.1685698E-02 1.678299 at 20iterations 4.1305781E-03 0.6026268 at 30iterations 1.7963467E-03 0.2609978 at 40iterations 7.8922551E-04 0.1126671 at 50iterations finished qdiffx linear iterations at : 20:00:55 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 7.8922551E-04 0.1126671 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 20:00:56 3.710u 0.132s 0:04.34 88.4% 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 20:00:56 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 = 5464 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2100000 grid size : 179 scale,in grids/A, set to be: 1.625868 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 1.625868 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.754056 assigned positive charge : 841.7791 centred at (gu) : 84.30347 87.60419 88.35413 assigned negative charge : -839.0311 centred at (gu) : 84.02779 87.57838 88.23193 start vw surface at 0.2800000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 115080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 36841 mr = 84067 m= 3906 mr = 26265 m= 130 mr = 1976 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.8700000 number of dielectric boundary points 43624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 495 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 40510 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) : 0.5419559 object centre at (A) : 35.58300 22.01850 30.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7256755E-02 1.7493704E-02 midg,1,midg; midg,igrid,midg 3.6891799E-03 8.6018443E-03 1,midg,midg; igrid,midg,midg -1.3927963E-02 1.1077451E-02 gauss-seidel spectral radius is 0.9983820 estimated iterations to convergence 197 setup time was (sec) 1.150000 now iterating at: 20:00:58 rms-change max change #iterations 4.788980 177.0798 at 10iterations 2.104211 63.07623 at 20iterations 0.9226999 26.81967 at 30iterations 0.4056912 13.93661 at 40iterations 0.1787116 4.794880 at 50iterations 7.9594254E-02 2.256027 at 60iterations 3.6346972E-02 1.006104 at 70iterations 1.7506434E-02 0.5267334 at 80iterations 9.3797725E-03 0.2790604 at 90iterations 5.7360483E-03 0.1769943 at 100iterations 3.8742926E-03 0.1132240 at 110iterations 2.7752698E-03 7.9746246E-02 at 120iterations finished qdiffx linear iterations at : 20:01:04 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.7752698E-03 7.9746246E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 20:01:05 7.903u 0.178s 0:08.40 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 20:01:05 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 = 5464 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2100000 grid size : 179 scale,in grids/A, set to be: 2.438802 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): 2.847000 68.31900 ymin,ymax (A): -8.841000 52.87800 zmin,zma (A): -2.314000 63.37400 x,y,z range (A): 65.47200 61.71900 65.68800 scale (grids/A): 2.438802 object centre (A): 35.58300 22.01850 30.53000 number of atom coordinates read : 5464 total number of charged atoms : 5294 net assigned charge : 2.754056 assigned positive charge : 841.7791 centred at (gu) : 81.45499 86.40574 87.53070 assigned negative charge : -839.0311 centred at (gu) : 81.04186 86.36763 87.34774 start vw surface at 0.2900000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 268196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 128464 mr = 204864 m= 37105 mr = 104454 m= 6167 mr = 28328 m= 486 mr = 4057 m= 6 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 128 time to turn everything in is 2.080000 number of dielectric boundary points 98467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 42285 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) : 1.625868 object centre at (A) : 35.58300 22.01850 30.53000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3337680 0.3701748 midg,1,midg; midg,igrid,midg -1.5426412E-02 4.6281211E-02 1,midg,midg; igrid,midg,midg -0.3955082 0.1712261 gauss-seidel spectral radius is 0.9992386 estimated iterations to convergence 286 setup time was (sec) 2.390000 now iterating at: 20:01:07 rms-change max change #iterations 12.26139 380.7424 at 10iterations 7.176765 153.1007 at 20iterations 4.172546 84.71931 at 30iterations 2.415053 50.10405 at 40iterations 1.395236 24.28378 at 50iterations 0.8048390 13.92886 at 60iterations 0.4615699 7.460433 at 70iterations 0.2653586 4.403208 at 80iterations 0.1521587 2.263489 at 90iterations 8.7765515E-02 1.381149 at 100iterations 5.0643656E-02 0.9022932 at 110iterations 2.9547166E-02 0.5089684 at 120iterations 1.7569069E-02 0.3129883 at 130iterations 1.0828986E-02 0.1961517 at 140iterations 7.0221745E-03 0.1357435 at 150iterations 4.8573324E-03 9.8491669E-02 at 160iterations 3.5805982E-03 6.6482544E-02 at 170iterations 2.7756675E-03 5.1109314E-02 at 180iterations finished qdiffx linear iterations at : 20:01:18 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 2.7756675E-03 5.1109314E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 20:01:18 13.065u 0.191s 0:13.64 97.1% 0+0k 0+0io 0pf+0w