Sat Oct 8 11:37:06 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 11:37:07 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: 254 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 : 512.2683 centred at (gu) : 90.41348 89.48857 91.06443 assigned negative charge : -517.2693 centred at (gu) : 90.23613 89.57906 91.06450 start vw surface at 0.1800000 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 = 0.2200000 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 0.5300000 number of grid points assigned charge 10722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8545528E-09 -7.5962863E-09 midg,1,midg; midg,igrid,midg 6.0729284E-09 -1.5890768E-08 1,midg,midg; igrid,midg,midg -2.6669483E-08 1.7744503E-08 gauss-seidel spectral radius is 0.9871182 estimated iterations to convergence 72 setup time was (sec) 0.6900000 now iterating at: 11:37:07 rms-change max change #iterations 0.1664393 21.60462 at 10iterations 1.6165616E-02 2.056389 at 20iterations 1.5828183E-03 0.2023926 at 30iterations 1.5451462E-04 1.8798828E-02 at 40iterations 1.4987314E-05 1.8119812E-03 at 50iterations finished qdiffx linear iterations at : 11:37:11 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 1.4987314E-05 1.8119812E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 11:37:11 4.202u 0.279s 0:04.92 90.8% 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 11:37:11 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: 254 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 : 512.2683 centred at (gu) : 91.23968 88.46449 93.19261 assigned negative charge : -517.2693 centred at (gu) : 90.70796 88.73641 93.19317 start vw surface at 0.1900000 fill in re-entrant regions at 0.3700000 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 -1.8184291E-02 -2.9388193E-02 midg,1,midg; midg,igrid,midg -1.8870145E-03 -5.2961826E-02 1,midg,midg; igrid,midg,midg -4.7143176E-02 1.5320426E-03 gauss-seidel spectral radius is 0.9986793 estimated iterations to convergence 218 setup time was (sec) 1.130000 now iterating at: 11:37:13 rms-change max change #iterations 4.991345 179.2114 at 10iterations 2.359654 72.15605 at 20iterations 1.123263 37.00896 at 30iterations 0.5348408 13.82364 at 40iterations 0.2527220 7.388807 at 50iterations 0.1203511 3.325504 at 60iterations 5.7166103E-02 1.686232 at 70iterations 2.7157141E-02 0.7928009 at 80iterations 1.2908938E-02 0.4110217 at 90iterations 6.1391029E-03 0.1704254 at 100iterations 2.9259359E-03 7.4989319E-02 at 110iterations 1.3896750E-03 3.6835313E-02 at 120iterations finished qdiffx linear iterations at : 11:37:21 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 1.3896750E-03 3.6835313E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.880000 DelPhi exited at 11:37:22 9.878u 0.296s 0:10.63 95.5% 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 11:37:22 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: 254 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 : 512.2683 centred at (gu) : 91.85909 87.69669 94.78870 assigned negative charge : -517.2693 centred at (gu) : 91.06187 88.10434 94.78967 start vw surface at 0.1900000 fill in re-entrant regions at 0.7200000 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 = 1.260000 no. cavity mid-points inaccessible to solvent = 27750 time to turn everything in is 2.110000 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 -0.2690900 -0.2788690 midg,1,midg; midg,igrid,midg -0.1664364 -0.6053717 1,midg,midg; igrid,midg,midg -0.4552958 -6.5856449E-02 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 2.450000 now iterating at: 11:37:25 rms-change max change #iterations 11.39477 407.0072 at 10iterations 6.626091 117.9621 at 20iterations 3.845082 64.57674 at 30iterations 2.227392 37.88736 at 40iterations 1.289458 22.60682 at 50iterations 0.7450900 11.19717 at 60iterations 0.4314303 6.495039 at 70iterations 0.2487064 4.078143 at 80iterations 0.1437633 2.130974 at 90iterations 8.3130978E-02 1.327026 at 100iterations 4.7931939E-02 0.8025684 at 110iterations 2.7677592E-02 0.4472694 at 120iterations 1.5980085E-02 0.2552490 at 130iterations 9.2362240E-03 0.1511374 at 140iterations 5.3286669E-03 8.4602356E-02 at 150iterations 3.0839969E-03 4.8210144E-02 at 160iterations 1.7785445E-03 2.8989792E-02 at 170iterations 1.0256740E-03 1.6069412E-02 at 180iterations finished qdiffx linear iterations at : 11:37:39 total time elapsed so far: 16.77000 # loops : 180 mean,max change (kT/e) : 1.0256740E-03 1.6069412E-02 energy calculations done at 16.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.95000 DelPhi exited at 11:37:40 16.951u 0.298s 0:17.63 97.7% 0+0k 0+0io 0pf+0w