Sat Oct 8 19:32:56 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 19:32:56 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7036130 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 0.7036130 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 88.43638 91.98219 90.72594 assigned negative charge : -390.7956 centred at (gu) : 88.31386 92.08919 90.65693 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8765 nv = 96 ne = 84 npr = 54749 no. pairs analyzed = 54749 no. exposed pairs = 3015 no. arc points = 21276 no. surface atoms = 1017 nbur = 1589 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 574 mr = 5128 m= 7 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 0.3100000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8425085E-09 8.4309455E-08 midg,1,midg; midg,igrid,midg 6.4084318E-08 -4.0846729E-08 1,midg,midg; igrid,midg,midg -4.9551634E-08 7.5724813E-08 gauss-seidel spectral radius is 0.9895223 estimated iterations to convergence 80 setup time was (sec) 0.5900000 now iterating at: 19:32:57 rms-change max change #iterations 0.2231887 34.93003 at 10iterations 2.7557645E-02 3.440125 at 20iterations 3.3987535E-03 0.4088326 at 30iterations 4.1441168E-04 6.1929703E-02 at 40iterations 5.1072879E-05 6.1661005E-03 at 50iterations finished qdiffx linear iterations at : 19:33:00 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 5.1072879E-05 6.1661005E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 19:33:01 4.496u 0.412s 0:05.17 94.7% 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 19:33:01 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.110839 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 2.110839 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 85.30882 95.94611 92.17742 assigned negative charge : -390.7956 centred at (gu) : 84.94126 96.26737 91.97057 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 92373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21276 grid for indexing accessible points = 1.400000 m= 37706 mr = 65798 m= 7798 mr = 29448 m= 785 mr = 5553 m= 27 mr = 421 m= 0 mr = 3 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 6596 time to turn everything in is 0.7500000 number of dielectric boundary points 37466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 19592 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) : 0.7036130 object centre at (A) : 19.00050 22.40800 15.94800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5050186E-02 2.0710994E-02 midg,1,midg; midg,igrid,midg -1.1948515E-03 -3.0016100E-02 1,midg,midg; igrid,midg,midg -9.7395182E-03 0.1114371 gauss-seidel spectral radius is 0.9988663 estimated iterations to convergence 235 setup time was (sec) 1.030000 now iterating at: 19:33:02 rms-change max change #iterations 5.258156 213.3500 at 10iterations 2.615006 82.50130 at 20iterations 1.309787 37.35811 at 30iterations 0.6555772 18.87002 at 40iterations 0.3294440 8.772827 at 50iterations 0.1644049 4.449579 at 60iterations 8.2526885E-02 2.348618 at 70iterations 4.1361678E-02 1.253447 at 80iterations 2.0692661E-02 0.5977440 at 90iterations 1.0412562E-02 0.2911265 at 100iterations 5.2174879E-03 0.1499863 at 110iterations 2.6164069E-03 6.7740440E-02 at 120iterations finished qdiffx linear iterations at : 19:33:12 total time elapsed so far: 10.98000 # loops : 120 mean,max change (kT/e) : 2.6164069E-03 6.7740440E-02 energy calculations done at 10.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 19:33:13 11.152u 0.469s 0:11.88 97.7% 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 19:33:13 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.166258 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 3.166258 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 394.9950 centred at (gu) : 82.96306 98.91898 93.26588 assigned negative charge : -390.7956 centred at (gu) : 82.41191 99.40108 92.95591 start vw surface at 0.1300000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 212598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21276 grid for indexing accessible points = 1.400000 m= 116307 mr = 157865 m= 49328 mr = 98143 m= 15208 mr = 41654 m= 3205 mr = 12299 m= 402 mr = 2475 m= 10 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 22342 time to turn everything in is 2.390000 number of dielectric boundary points 84353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 19724 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) : 2.110839 object centre at (A) : 19.00050 22.40800 15.94800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4367878 0.1548083 midg,1,midg; midg,igrid,midg -9.4387054E-02 -0.1935175 1,midg,midg; igrid,midg,midg -0.1379267 1.568330 gauss-seidel spectral radius is 0.9993129 estimated iterations to convergence 301 setup time was (sec) 2.730000 now iterating at: 19:33:16 rms-change max change #iterations 11.51277 395.9724 at 10iterations 6.780709 132.2897 at 20iterations 3.990787 75.54154 at 30iterations 2.343679 42.23434 at 40iterations 1.377803 24.02866 at 50iterations 0.8099163 13.03241 at 60iterations 0.4754340 7.448809 at 70iterations 0.2792797 4.464396 at 80iterations 0.1637988 2.548615 at 90iterations 9.6040070E-02 1.593376 at 100iterations 5.6327485E-02 0.8842850 at 110iterations 3.3069771E-02 0.5660629 at 120iterations 1.9370751E-02 0.3136132 at 130iterations 1.1372514E-02 0.1786041 at 140iterations 6.6837599E-03 0.1073551 at 150iterations 3.9188606E-03 6.5505505E-02 at 160iterations 2.3015139E-03 3.6899567E-02 at 170iterations 1.3512251E-03 2.1438599E-02 at 180iterations finished qdiffx linear iterations at : 19:33:33 total time elapsed so far: 19.63000 # loops : 180 mean,max change (kT/e) : 1.3512251E-03 2.1438599E-02 energy calculations done at 19.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.79000 DelPhi exited at 19:33:33 19.798u 0.471s 0:20.53 98.6% 0+0k 0+0io 0pf+0w