Sat Oct 8 11:41:34 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 11:41:34 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 = 5354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5265415 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 0.5265415 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5184 net assigned charge : 0.5000382 assigned positive charge : 812.9066 centred at (gu) : 90.35576 90.89494 91.20448 assigned negative charge : -812.4124 centred at (gu) : 90.29513 90.87994 91.24599 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 9140 nv = 96 ne = 84 npr = 111268 no. pairs analyzed = 111268 no. exposed pairs = 6314 no. arc points = 42971 no. surface atoms = 2123 nbur = 3231 mkacc time = 0.3200000 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= 328 mr = 4974 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 4486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4249 ## 553 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 12338 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8366052E-10 -3.0593311E-10 midg,1,midg; midg,igrid,midg -5.5878000E-11 1.2675590E-10 1,midg,midg; igrid,midg,midg -3.0383931E-10 3.9278869E-10 gauss-seidel spectral radius is 0.9815796 estimated iterations to convergence 61 setup time was (sec) 0.9400000 now iterating at: 11:41:35 rms-change max change #iterations 8.5290141E-02 11.58675 at 10iterations 6.7702383E-03 1.344955 at 20iterations 1.1821248E-03 0.2990112 at 30iterations 3.0312117E-04 7.3051453E-02 at 40iterations 8.2291466E-05 1.8554688E-02 at 50iterations finished qdiffx linear iterations at : 11:41:38 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 8.2291466E-05 1.8554688E-02 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 11:41:39 4.335u 0.195s 0:04.93 91.6% 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 8 2011 at 11:41:39 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 = 5354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.579625 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 1.579625 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5184 net assigned charge : 0.5000382 assigned positive charge : 812.9066 centred at (gu) : 91.06559 92.68328 93.61195 assigned negative charge : -812.4124 centred at (gu) : 90.88493 92.63947 93.73790 start vw surface at 0.2800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 103309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 30796 mr = 72740 m= 2888 mr = 21119 m= 57 mr = 1306 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 0.9600000 number of dielectric boundary points 41882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 507 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 39310 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) : 0.5265415 object centre at (A) : 39.88000 35.05250 42.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3183983E-02 -3.3974457E-03 midg,1,midg; midg,igrid,midg 8.0257969E-04 1.7647067E-02 1,midg,midg; igrid,midg,midg -1.0944838E-02 9.1239121E-03 gauss-seidel spectral radius is 0.9982771 estimated iterations to convergence 191 setup time was (sec) 1.330000 now iterating at: 11:41:40 rms-change max change #iterations 4.371753 168.8360 at 10iterations 1.858811 56.39511 at 20iterations 0.7928027 22.83474 at 30iterations 0.3391410 10.42186 at 40iterations 0.1447337 4.710966 at 50iterations 6.2260594E-02 1.876289 at 60iterations 2.6850661E-02 0.7529602 at 70iterations 1.1644152E-02 0.3469543 at 80iterations 5.0932677E-03 0.1699219 at 90iterations 2.2978827E-03 8.1024170E-02 at 100iterations 1.0811710E-03 4.1030884E-02 at 110iterations 5.4165622E-04 2.3941040E-02 at 120iterations finished qdiffx linear iterations at : 11:41:48 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 5.4165622E-04 2.3941040E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 11:41:49 9.667u 0.287s 0:10.49 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 11:41:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.369437 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): 7.364000 72.39600 ymin,ymax (A): 1.247000 68.85800 zmin,zma (A): 9.486000 75.36300 x,y,z range (A): 65.03200 67.61100 65.87700 scale (grids/A): 2.369437 object centre (A): 39.88000 35.05250 42.42450 number of atom coordinates read : 5354 total number of charged atoms : 5184 net assigned charge : 0.5000382 assigned positive charge : 812.9066 centred at (gu) : 91.59798 94.02429 95.41757 assigned negative charge : -812.4124 centred at (gu) : 91.32732 93.95921 95.60674 start vw surface at 0.2600000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 241314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 108797 mr = 179073 m= 29504 mr = 85695 m= 4248 mr = 21916 m= 250 mr = 2721 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 3433 time to turn everything in is 2.230000 number of dielectric boundary points 94618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 2.410000 number of grid points assigned charge 41402 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) : 1.579625 object centre at (A) : 39.88000 35.05250 42.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2174520 -0.2396335 midg,1,midg; midg,igrid,midg 3.9829925E-02 0.1792531 1,midg,midg; igrid,midg,midg -0.2131685 5.5055059E-02 gauss-seidel spectral radius is 0.9992176 estimated iterations to convergence 282 setup time was (sec) 2.600000 now iterating at: 11:41:52 rms-change max change #iterations 11.64188 337.0294 at 10iterations 6.848190 163.0255 at 20iterations 4.009738 96.87481 at 30iterations 2.334564 61.21217 at 40iterations 1.351192 27.84668 at 50iterations 0.7806707 15.32415 at 60iterations 0.4493687 9.213821 at 70iterations 0.2580472 5.492701 at 80iterations 0.1482913 3.073782 at 90iterations 8.4891267E-02 1.654963 at 100iterations 4.8542444E-02 0.8941841 at 110iterations 2.7803427E-02 0.5875702 at 120iterations 1.5899496E-02 0.2874603 at 130iterations 9.1103846E-03 0.1735215 at 140iterations 5.2182311E-03 0.1057973 at 150iterations 3.0071847E-03 5.0127983E-02 at 160iterations 1.7368424E-03 3.0059576E-02 at 170iterations 1.0168582E-03 1.8709183E-02 at 180iterations finished qdiffx linear iterations at : 11:42:05 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 1.0168582E-03 1.8709183E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.61000 DelPhi exited at 11:42:05 15.609u 0.249s 0:16.15 98.0% 0+0k 0+0io 0pf+0w