Sat Oct 8 17:47:30 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+sph.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 = amb.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 17:47:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 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: 0.5237142 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): 40.78800 108.7640 ymin,ymax (A): 8.684000 60.01700 zmin,zma (A): 3.241000 49.53200 x,y,z range (A): 67.97600 51.33300 46.29100 scale (grids/A): 0.5237142 object centre (A): 74.77600 34.35050 26.38650 number of atom coordinates read : 3297 total number of charged atoms : 3153 net assigned charge : -4.499992 assigned positive charge : 492.7628 centred at (gu) : 90.26115 88.66542 90.12995 assigned negative charge : -497.2640 centred at (gu) : 90.22780 88.59130 90.14676 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5884 nv = 96 ne = 84 npr = 66225 no. pairs analyzed = 66225 no. exposed pairs = 4018 no. arc points = 27868 no. surface atoms = 1366 nbur = 1931 mkacc time = 0.1900000 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= 212 mr = 3155 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.4000000 number of dielectric boundary points 2932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2788 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7716 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5546481E-11 -1.6740717E-10 midg,1,midg; midg,igrid,midg -4.8466531E-10 8.3017634E-11 1,midg,midg; igrid,midg,midg -2.0007440E-10 -6.1510541E-12 gauss-seidel spectral radius is 0.9812416 estimated iterations to convergence 60 setup time was (sec) 0.6600000 now iterating at: 17:47:31 rms-change max change #iterations 6.3599423E-02 11.37714 at 10iterations 3.7980108E-03 0.6550560 at 20iterations 2.4080412E-04 3.9100647E-02 at 30iterations 2.5777310E-05 6.0062408E-03 at 40iterations 5.8421269E-06 1.5239716E-03 at 50iterations finished qdiffx linear iterations at : 17:47:34 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 5.8421269E-06 1.5239716E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 17:47:35 4.125u 0.280s 0:04.66 94.4% 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 Sat Oct 8 2011 at 17:47:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 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: 1.571143 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): 40.78800 108.7640 ymin,ymax (A): 8.684000 60.01700 zmin,zma (A): 3.241000 49.53200 x,y,z range (A): 67.97600 51.33300 46.29100 scale (grids/A): 1.571143 object centre (A): 74.77600 34.35050 26.38650 number of atom coordinates read : 3297 total number of charged atoms : 3153 net assigned charge : -4.499992 assigned positive charge : 492.7628 centred at (gu) : 90.78278 85.99577 90.38927 assigned negative charge : -497.2640 centred at (gu) : 90.68307 85.77357 90.44018 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27868 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20311 mr = 46407 m= 1810 mr = 13940 m= 32 mr = 796 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.6000000 number of dielectric boundary points 27324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23878 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) : 0.5237142 object centre at (A) : 74.77600 34.35050 26.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1089766E-03 -4.3025580E-03 midg,1,midg; midg,igrid,midg -7.1766046E-03 1.3472347E-03 1,midg,midg; igrid,midg,midg 1.2096125E-02 -3.9931806E-03 gauss-seidel spectral radius is 0.9980618 estimated iterations to convergence 181 setup time was (sec) 0.8800000 now iterating at: 17:47:36 rms-change max change #iterations 3.219129 149.7759 at 10iterations 1.307338 54.47803 at 20iterations 0.5285699 19.20175 at 30iterations 0.2142363 8.527176 at 40iterations 8.7238483E-02 3.249724 at 50iterations 3.5298415E-02 1.345513 at 60iterations 1.4394069E-02 0.5322661 at 70iterations 5.8391383E-03 0.2432480 at 80iterations 2.3825865E-03 8.8764191E-02 at 90iterations 9.6934818E-04 3.5758972E-02 at 100iterations 4.0199386E-04 1.5712738E-02 at 110iterations 1.6891766E-04 6.3315630E-03 at 120iterations finished qdiffx linear iterations at : 17:47:44 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 1.6891766E-04 6.3315630E-03 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 17:47:45 9.167u 0.311s 0:09.83 96.3% 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 17:47:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 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: 2.356714 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): 40.78800 108.7640 ymin,ymax (A): 8.684000 60.01700 zmin,zma (A): 3.241000 49.53200 x,y,z range (A): 67.97600 51.33300 46.29100 scale (grids/A): 2.356714 object centre (A): 74.77600 34.35050 26.38650 number of atom coordinates read : 3297 total number of charged atoms : 3153 net assigned charge : -4.499992 assigned positive charge : 492.7628 centred at (gu) : 91.17376 83.99343 90.58361 assigned negative charge : -497.2640 centred at (gu) : 91.02426 83.66027 90.66015 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 154408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27868 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 71740 mr = 113407 m= 18827 mr = 57009 m= 2603 mr = 13951 m= 129 mr = 1580 m= 0 mr = 41 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 2044 time to turn everything in is 1.440000 number of dielectric boundary points 61719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 25180 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) : 1.571143 object centre at (A) : 74.77600 34.35050 26.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4783278E-02 -6.4158268E-02 midg,1,midg; midg,igrid,midg -0.1037065 3.8444314E-02 1,midg,midg; igrid,midg,midg 0.5795006 -0.1267227 gauss-seidel spectral radius is 0.9991015 estimated iterations to convergence 264 setup time was (sec) 1.750000 now iterating at: 17:47:47 rms-change max change #iterations 8.510639 259.8453 at 10iterations 4.704787 106.6899 at 20iterations 2.587442 58.52020 at 30iterations 1.417361 31.42883 at 40iterations 0.7772033 16.35324 at 50iterations 0.4233729 10.21474 at 60iterations 0.2302844 4.945550 at 70iterations 0.1254472 2.632317 at 80iterations 6.8229839E-02 1.412419 at 90iterations 3.7082803E-02 0.7583065 at 100iterations 2.0174494E-02 0.4538553 at 110iterations 1.0943975E-02 0.2271376 at 120iterations 5.9577408E-03 0.1221018 at 130iterations 3.2389876E-03 6.1931610E-02 at 140iterations 1.7672895E-03 3.4458637E-02 at 150iterations 9.6613314E-04 2.0146370E-02 at 160iterations 5.3270662E-04 1.0741234E-02 at 170iterations 2.9644507E-04 5.9471130E-03 at 180iterations finished qdiffx linear iterations at : 17:48:00 total time elapsed so far: 14.88000 # loops : 180 mean,max change (kT/e) : 2.9644507E-04 5.9471130E-03 energy calculations done at 14.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.05000 DelPhi exited at 17:48:00 15.056u 0.317s 0:15.64 98.2% 0+0k 0+0io 0pf+0w