Tue Oct 11 03:40:49 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 Tue Oct 11 2011 at 03:40:49 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6493270 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 0.6493270 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.9438 centred at (gu) : 91.93746 90.38810 90.51367 assigned negative charge : -417.1723 centred at (gu) : 91.73174 90.55701 90.56087 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7830 nv = 96 ne = 84 npr = 55814 no. pairs analyzed = 55814 no. exposed pairs = 3400 no. arc points = 23977 no. surface atoms = 1140 nbur = 1625 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4351 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2389 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9322 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2725130E-08 -1.1491954E-09 midg,1,midg; midg,igrid,midg 3.0619496E-08 -2.2850477E-08 1,midg,midg; igrid,midg,midg -1.7839410E-08 5.9121128E-08 gauss-seidel spectral radius is 0.9877242 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 03:40:50 rms-change max change #iterations 0.1610096 21.93538 at 10iterations 1.6856456E-02 2.325865 at 20iterations 1.8586840E-03 0.2477417 at 30iterations 2.8125421E-04 3.4180641E-02 at 40iterations 7.0406910E-05 7.6694489E-03 at 50iterations finished qdiffx linear iterations at : 03:40:54 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 7.0406910E-05 7.6694489E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 03:40:54 4.470u 0.394s 0:05.28 92.0% 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 Tue Oct 11 2011 at 03:40:54 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.947981 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 1.947981 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.9438 centred at (gu) : 95.81223 91.16377 91.54035 assigned negative charge : -417.1723 centred at (gu) : 95.19476 91.67099 91.68252 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23977 grid for indexing accessible points = 1.400000 m= 32206 mr = 58218 m= 5503 mr = 24160 m= 370 mr = 3543 m= 7 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.6800000 number of dielectric boundary points 35677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20642 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) : 0.6493270 object centre at (A) : 37.76500 20.96350 19.90450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1004428E-02 -2.4246989E-02 midg,1,midg; midg,igrid,midg 3.1956166E-02 -8.0479998E-03 1,midg,midg; igrid,midg,midg -8.4455535E-03 8.2677431E-02 gauss-seidel spectral radius is 0.9987118 estimated iterations to convergence 221 setup time was (sec) 0.9900000 now iterating at: 03:40:56 rms-change max change #iterations 4.590342 198.3114 at 10iterations 2.206819 72.67415 at 20iterations 1.056632 32.65057 at 30iterations 0.5057763 15.81101 at 40iterations 0.2426430 8.366001 at 50iterations 0.1162234 4.164615 at 60iterations 5.5744130E-02 1.719122 at 70iterations 2.6733369E-02 0.8379000 at 80iterations 1.2923434E-02 0.4152470 at 90iterations 6.2078964E-03 0.2049522 at 100iterations 3.0003996E-03 9.7795486E-02 at 110iterations 1.4700015E-03 4.6253204E-02 at 120iterations finished qdiffx linear iterations at : 03:41:06 total time elapsed so far: 10.77000 # loops : 120 mean,max change (kT/e) : 1.4700015E-03 4.6253204E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 03:41:06 10.942u 0.434s 0:11.89 95.6% 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 Tue Oct 11 2011 at 03:41:06 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.921971 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 2.921971 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.9438 centred at (gu) : 98.71802 91.74564 92.31049 assigned negative charge : -417.1723 centred at (gu) : 97.79223 92.50625 92.52356 start vw surface at 0.1300000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 192763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23977 grid for indexing accessible points = 1.400000 m= 101699 mr = 140377 m= 39395 mr = 83928 m= 10029 mr = 32095 m= 1610 mr = 7672 m= 115 mr = 1101 m= 0 mr = 55 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 2292 time to turn everything in is 1.830000 number of dielectric boundary points 80383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 20935 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) : 1.947981 object centre at (A) : 37.76500 20.96350 19.90450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1178119 -0.3780895 midg,1,midg; midg,igrid,midg 0.4309437 5.8188174E-02 1,midg,midg; igrid,midg,midg -6.8619162E-02 0.7819753 gauss-seidel spectral radius is 0.9992811 estimated iterations to convergence 294 setup time was (sec) 2.180000 now iterating at: 03:41:09 rms-change max change #iterations 10.65396 584.5649 at 10iterations 6.278309 148.9546 at 20iterations 3.677611 76.52170 at 30iterations 2.155757 38.72038 at 40iterations 1.258432 22.81289 at 50iterations 0.7342516 12.51294 at 60iterations 0.4276697 7.791178 at 70iterations 0.2487635 4.437551 at 80iterations 0.1447951 2.554672 at 90iterations 8.4294654E-02 1.444366 at 100iterations 4.8938788E-02 0.9123917 at 110iterations 2.8512947E-02 0.4933913 at 120iterations 1.6623683E-02 0.3298440 at 130iterations 9.7103622E-03 0.1777420 at 140iterations 5.7002534E-03 0.1263661 at 150iterations 3.3837529E-03 5.9665680E-02 at 160iterations 2.0418954E-03 3.7471771E-02 at 170iterations 1.2677982E-03 2.1678925E-02 at 180iterations finished qdiffx linear iterations at : 03:41:26 total time elapsed so far: 18.98000 # loops : 180 mean,max change (kT/e) : 1.2677982E-03 2.1678925E-02 energy calculations done at 18.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 03:41:26 19.163u 0.457s 0:20.01 98.0% 0+0k 0+0io 0pf+0w