Mon Oct 10 09:45:18 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 Mon Oct 10 2011 at 09:45:18 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5817184 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 0.5817184 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.014017 assigned positive charge : 391.5402 centred at (gu) : 88.02419 88.71489 88.00290 assigned negative charge : -384.5266 centred at (gu) : 88.06858 88.59725 87.96642 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6238 nv = 96 ne = 84 npr = 50801 no. pairs analyzed = 50801 no. exposed pairs = 4131 no. arc points = 30474 no. surface atoms = 1358 nbur = 1312 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 = 1.484000 m= 350 mr = 2667 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3040 ## 319 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4116115E-09 1.5023983E-09 midg,1,midg; midg,igrid,midg -1.0340789E-09 2.9360503E-09 1,midg,midg; igrid,midg,midg 3.9931920E-09 4.9622451E-10 gauss-seidel spectral radius is 0.9847445 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 09:45:19 rms-change max change #iterations 9.0541922E-02 15.66660 at 10iterations 7.0036775E-03 1.177058 at 20iterations 5.5991055E-04 8.8184357E-02 at 30iterations 4.6368405E-05 7.1916580E-03 at 40iterations 5.1751772E-06 7.5912476E-04 at 50iterations finished qdiffx linear iterations at : 09:45:22 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.1751772E-06 7.5912476E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 09:45:22 3.410u 0.182s 0:03.86 93.0% 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 Mon Oct 10 2011 at 09:45:22 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.745155 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 1.745155 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.014017 assigned positive charge : 391.5402 centred at (gu) : 84.07202 86.14422 84.00815 assigned negative charge : -384.5266 centred at (gu) : 84.20541 85.79157 83.89919 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30474 grid for indexing accessible points = 1.400000 m= 21560 mr = 39893 m= 3073 mr = 13559 m= 122 mr = 1414 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 36282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19638 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) : 0.5817184 object centre at (A) : 8.402999 -32.13750 30.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3520614E-03 2.5280800E-03 midg,1,midg; midg,igrid,midg 2.3622248E-02 3.1877015E-02 1,midg,midg; igrid,midg,midg 3.7547187E-03 1.7145708E-03 gauss-seidel spectral radius is 0.9984151 estimated iterations to convergence 199 setup time was (sec) 0.5600000 now iterating at: 09:45:23 rms-change max change #iterations 3.555113 180.2984 at 10iterations 1.555215 58.45307 at 20iterations 0.6856971 24.67693 at 30iterations 0.3007698 10.32379 at 40iterations 0.1318087 5.491692 at 50iterations 5.8069974E-02 2.082167 at 60iterations 2.5575625E-02 0.9599972 at 70iterations 1.1215283E-02 0.3960838 at 80iterations 4.9321041E-03 0.1768703 at 90iterations 2.1805493E-03 7.8456879E-02 at 100iterations 9.5691846E-04 3.4380913E-02 at 110iterations 4.2322479E-04 1.3877869E-02 at 120iterations finished qdiffx linear iterations at : 09:45:30 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 4.2322479E-04 1.3877869E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 09:45:30 7.850u 0.198s 0:08.49 94.6% 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 Mon Oct 10 2011 at 09:45:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.617733 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): -17.50900 34.31500 ymin,ymax (A): -61.68100 -2.594000 zmin,zma (A): -0.4859999 60.71200 x,y,z range (A): 51.82400 59.08700 61.19800 scale (grids/A): 2.617733 object centre (A): 8.402999 -32.13750 30.11300 number of atom coordinates read : 2670 total number of charged atoms : 2525 net assigned charge : 7.014017 assigned positive charge : 391.5402 centred at (gu) : 81.10792 84.21628 81.01214 assigned negative charge : -384.5266 centred at (gu) : 81.30815 83.68735 80.84871 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 153125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30474 grid for indexing accessible points = 1.400000 m= 69632 mr = 98717 m= 23578 mr = 51292 m= 5004 mr = 16718 m= 464 mr = 3013 m= 20 mr = 195 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 81884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20193 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) : 1.745155 object centre at (A) : 8.402999 -32.13750 30.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2169724 1.4714186E-02 midg,1,midg; midg,igrid,midg 0.4590088 0.3542757 1,midg,midg; igrid,midg,midg -6.3631497E-02 1.1519617E-02 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.070000 now iterating at: 09:45:32 rms-change max change #iterations 9.107060 304.7532 at 10iterations 5.410533 151.9171 at 20iterations 3.157577 76.14342 at 30iterations 1.835401 44.14812 at 40iterations 1.058129 32.72251 at 50iterations 0.6085122 14.05645 at 60iterations 0.3487596 8.101265 at 70iterations 0.1995506 4.308424 at 80iterations 0.1138565 2.401574 at 90iterations 6.4936221E-02 1.353848 at 100iterations 3.6981508E-02 0.7805176 at 110iterations 2.1056041E-02 0.4588165 at 120iterations 1.1939934E-02 0.2419853 at 130iterations 6.8045817E-03 0.1419058 at 140iterations 3.8548654E-03 7.7449799E-02 at 150iterations 2.1843945E-03 4.3398619E-02 at 160iterations 1.2403963E-03 2.2773743E-02 at 170iterations 7.0389581E-04 1.5049934E-02 at 180iterations finished qdiffx linear iterations at : 09:45:43 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 7.0389581E-04 1.5049934E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 09:45:44 12.704u 0.221s 0:13.21 97.8% 0+0k 0+0io 0pf+0w