Sat Oct 15 12:50:07 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 15 2011 at 12:50:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 !!! WARNING: HIR 219 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5215124 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 0.5215124 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.014022 assigned positive charge : 391.0234 centred at (gu) : 90.54758 93.38063 91.45341 assigned negative charge : -390.0107 centred at (gu) : 90.51766 93.34538 91.54899 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4844 nv = 96 ne = 84 npr = 53004 no. pairs analyzed = 53004 no. exposed pairs = 3726 no. arc points = 26614 no. surface atoms = 1237 nbur = 1460 mkacc time = 9.0000004E-02 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 = 1.624000 m= 188 mr = 2286 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5794271E-10 -2.7895164E-10 midg,1,midg; midg,igrid,midg -2.2572064E-11 2.4497834E-10 1,midg,midg; igrid,midg,midg -3.7088835E-11 1.0185891E-10 gauss-seidel spectral radius is 0.9810534 estimated iterations to convergence 60 setup time was (sec) 0.3700000 now iterating at: 12:50:08 rms-change max change #iterations 5.5589139E-02 10.47179 at 10iterations 3.2568667E-03 0.6584244 at 20iterations 1.9996404E-04 3.7742615E-02 at 30iterations 1.5464659E-05 3.7956238E-03 at 40iterations 2.1393496E-06 5.3656101E-04 at 50iterations finished qdiffx linear iterations at : 12:50:11 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.1393496E-06 5.3656101E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 12:50:11 3.572u 0.236s 0:04.24 89.6% 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 15 2011 at 12:50:11 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 !!! WARNING: HIR 219 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.564537 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 1.564537 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.014022 assigned positive charge : 391.0234 centred at (gu) : 91.64201 100.1412 94.35955 assigned negative charge : -390.0107 centred at (gu) : 91.55280 100.0362 94.64697 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 15332 mr = 33809 m= 1570 mr = 10155 m= 34 mr = 755 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 509 time to turn everything in is 0.2800000 number of dielectric boundary points 25490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 19369 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) : 0.5215124 object centre at (A) : 101.5855 14.58350 89.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0310326E-03 1.4411288E-03 midg,1,midg; midg,igrid,midg -3.4970297E-03 -4.4016894E-03 1,midg,midg; igrid,midg,midg -5.5454538E-04 6.2759891E-03 gauss-seidel spectral radius is 0.9979942 estimated iterations to convergence 178 setup time was (sec) 0.5300000 now iterating at: 12:50:12 rms-change max change #iterations 2.799144 196.3717 at 10iterations 1.111329 49.30213 at 20iterations 0.4399274 18.32421 at 30iterations 0.1750637 6.871397 at 40iterations 6.9468126E-02 3.108160 at 50iterations 2.7814562E-02 1.096729 at 60iterations 1.1050702E-02 0.4127388 at 70iterations 4.4155926E-03 0.1734314 at 80iterations 1.7624400E-03 7.4327469E-02 at 90iterations 7.0406130E-04 2.8002739E-02 at 100iterations 2.8202293E-04 1.3069153E-02 at 110iterations 1.1301506E-04 4.7206879E-03 at 120iterations finished qdiffx linear iterations at : 12:50:20 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 1.1301506E-04 4.7206879E-03 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 12:50:21 8.383u 0.276s 0:09.51 90.9% 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 15 2011 at 12:50:21 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 = 2697 !!! WARNING: HIR 219 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.346806 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): 76.90200 126.2690 ymin,ymax (A): -19.54800 48.71500 zmin,zma (A): 64.35900 114.4860 x,y,z range (A): 49.36700 68.26300 50.12700 scale (grids/A): 2.346806 object centre (A): 101.5855 14.58350 89.42250 number of atom coordinates read : 2697 total number of charged atoms : 2555 net assigned charge : 1.014022 assigned positive charge : 391.0234 centred at (gu) : 92.46268 105.2115 96.53908 assigned negative charge : -390.0107 centred at (gu) : 92.32918 105.0541 96.97041 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 124091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 52814 mr = 83842 m= 15234 mr = 40319 m= 2398 mr = 11299 m= 107 mr = 1525 m= 0 mr = 24 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1557 time to turn everything in is 0.6500000 number of dielectric boundary points 57635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20406 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) : 1.564537 object centre at (A) : 101.5855 14.58350 89.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6125751E-02 3.8017537E-02 midg,1,midg; midg,igrid,midg -2.5513798E-02 -5.9263144E-02 1,midg,midg; igrid,midg,midg -4.3355771E-03 0.1111919 gauss-seidel spectral radius is 0.9990730 estimated iterations to convergence 260 setup time was (sec) 0.9000000 now iterating at: 12:50:22 rms-change max change #iterations 7.470714 286.8112 at 10iterations 4.093790 123.2460 at 20iterations 2.226379 65.55539 at 30iterations 1.206675 32.95440 at 40iterations 0.6530902 15.64918 at 50iterations 0.3519030 8.614872 at 60iterations 0.1895628 4.685223 at 70iterations 0.1021314 2.526390 at 80iterations 5.4801725E-02 1.217350 at 90iterations 2.9412448E-02 0.6902599 at 100iterations 1.5821565E-02 0.3721581 at 110iterations 8.4655369E-03 0.2250500 at 120iterations 4.5619360E-03 0.1072936 at 130iterations 2.4437460E-03 5.4927826E-02 at 140iterations 1.3108447E-03 2.9017448E-02 at 150iterations 7.0075889E-04 1.7463684E-02 at 160iterations 3.7732214E-04 8.7394714E-03 at 170iterations 2.0203984E-04 4.7590584E-03 at 180iterations finished qdiffx linear iterations at : 12:50:35 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 2.0203984E-04 4.7590584E-03 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 12:50:35 13.106u 0.292s 0:14.05 95.3% 0+0k 0+0io 0pf+0w