Sun Oct 9 10:37:09 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 10:37:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 217 has a net charge of 0.5140 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: 0.6330127 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): 1.583000 57.82200 ymin,ymax (A): -28.83900 24.85000 zmin,zma (A): -24.43500 26.92500 x,y,z range (A): 56.23900 53.68900 51.36000 scale (grids/A): 0.6330127 object centre (A): 29.70250 -1.994499 1.245001 number of atom coordinates read : 2581 total number of charged atoms : 2440 net assigned charge : -2.485962 assigned positive charge : 374.3375 centred at (gu) : 89.14998 89.21466 91.21368 assigned negative charge : -376.8248 centred at (gu) : 89.16578 89.35432 91.34095 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7130 nv = 96 ne = 84 npr = 51236 no. pairs analyzed = 51236 no. exposed pairs = 3661 no. arc points = 26158 no. surface atoms = 1229 nbur = 1352 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3521 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2418 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7146000E-09 -1.9487810E-08 midg,1,midg; midg,igrid,midg 1.1832017E-08 -1.3582004E-08 1,midg,midg; igrid,midg,midg -1.6870036E-09 -3.6522687E-09 gauss-seidel spectral radius is 0.9870874 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 10:37:10 rms-change max change #iterations 0.1312521 18.72204 at 10iterations 1.2789021E-02 2.009129 at 20iterations 1.2363137E-03 0.1947708 at 30iterations 1.2285882E-04 2.1276474E-02 at 40iterations 1.4183366E-05 2.0942688E-03 at 50iterations finished qdiffx linear iterations at : 10:37:12 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.4183366E-05 2.0942688E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 10:37:13 3.072u 0.139s 0:03.50 91.4% 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 10:37:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 217 has a net charge of 0.5140 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: 1.899038 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): 1.583000 57.82200 ymin,ymax (A): -28.83900 24.85000 zmin,zma (A): -24.43500 26.92500 x,y,z range (A): 56.23900 53.68900 51.36000 scale (grids/A): 1.899038 object centre (A): 29.70250 -1.994499 1.245001 number of atom coordinates read : 2581 total number of charged atoms : 2440 net assigned charge : -2.485962 assigned positive charge : 374.3375 centred at (gu) : 87.44917 87.64319 93.64035 assigned negative charge : -376.8248 centred at (gu) : 87.49743 88.06264 94.02265 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26158 grid for indexing accessible points = 1.400000 m= 26248 mr = 49569 m= 4519 mr = 18106 m= 312 mr = 2727 m= 4 mr = 131 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 36761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19208 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) : 0.6330127 object centre at (A) : 29.70250 -1.994499 1.245001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1504343E-03 -4.4638798E-02 midg,1,midg; midg,igrid,midg 3.6849651E-02 -1.1490536E-02 1,midg,midg; igrid,midg,midg 2.9494776E-03 -9.2572402E-03 gauss-seidel spectral radius is 0.9986478 estimated iterations to convergence 215 setup time was (sec) 0.8000000 now iterating at: 10:37:14 rms-change max change #iterations 4.159974 169.3076 at 10iterations 1.934301 76.90102 at 20iterations 0.9080932 33.54758 at 30iterations 0.4246927 12.85678 at 40iterations 0.1996727 6.124775 at 50iterations 9.3338199E-02 2.964920 at 60iterations 4.3911658E-02 1.414593 at 70iterations 2.0621229E-02 0.6242934 at 80iterations 9.6639758E-03 0.3779011 at 90iterations 4.5445920E-03 0.1407013 at 100iterations 2.1345946E-03 7.1075439E-02 at 110iterations 9.9863927E-04 3.3363819E-02 at 120iterations finished qdiffx linear iterations at : 10:37:20 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 9.9863927E-04 3.3363819E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 10:37:20 6.941u 0.161s 0:07.38 96.2% 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 Sun Oct 9 2011 at 10:37:20 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIR 217 has a net charge of 0.5140 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: 2.848557 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): 1.583000 57.82200 ymin,ymax (A): -28.83900 24.85000 zmin,zma (A): -24.43500 26.92500 x,y,z range (A): 56.23900 53.68900 51.36000 scale (grids/A): 2.848557 object centre (A): 29.70250 -1.994499 1.245001 number of atom coordinates read : 2581 total number of charged atoms : 2440 net assigned charge : -2.485962 assigned positive charge : 374.3375 centred at (gu) : 86.17368 86.46460 95.46033 assigned negative charge : -376.8248 centred at (gu) : 86.24613 87.09399 96.03398 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 176410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26158 grid for indexing accessible points = 1.400000 m= 83715 mr = 121327 m= 30763 mr = 65523 m= 8160 mr = 23748 m= 1298 mr = 5840 m= 73 mr = 885 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 83062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19519 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) : 1.899038 object centre at (A) : 29.70250 -1.994499 1.245001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1357868 -0.4475796 midg,1,midg; midg,igrid,midg 0.3977396 -7.0809305E-02 1,midg,midg; igrid,midg,midg -4.2603691E-03 -3.7800122E-02 gauss-seidel spectral radius is 0.9992709 estimated iterations to convergence 292 setup time was (sec) 1.680000 now iterating at: 10:37:22 rms-change max change #iterations 9.904628 322.4097 at 10iterations 5.876759 134.1259 at 20iterations 3.462559 76.14944 at 30iterations 2.029020 39.37823 at 40iterations 1.185879 23.15295 at 50iterations 0.6896613 13.51138 at 60iterations 0.4007602 7.729200 at 70iterations 0.2331012 4.332318 at 80iterations 0.1350644 2.620277 at 90iterations 7.8187212E-02 1.401050 at 100iterations 4.5263950E-02 0.8628788 at 110iterations 2.6199674E-02 0.5056839 at 120iterations 1.5147938E-02 0.2889709 at 130iterations 8.7545719E-03 0.1559610 at 140iterations 5.0478955E-03 8.9659691E-02 at 150iterations 2.9225117E-03 5.2425385E-02 at 160iterations 1.6889352E-03 3.0048370E-02 at 170iterations 9.7681652E-04 1.7179489E-02 at 180iterations finished qdiffx linear iterations at : 10:37:32 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 9.7681652E-04 1.7179489E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 10:37:33 12.383u 0.226s 0:13.02 96.7% 0+0k 0+0io 0pf+0w