Sat Oct 8 14:32:29 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 14:32:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2987 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6411295 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): -11.49800 42.43500 ymin,ymax (A): -22.17400 22.64400 zmin,zma (A): -7.213000 48.31400 x,y,z range (A): 53.93300 44.81800 55.52700 scale (grids/A): 0.6411295 object centre (A): 15.46850 0.2349997 20.55050 number of atom coordinates read : 2987 total number of charged atoms : 2842 net assigned charge : 3.000005 assigned positive charge : 449.8027 centred at (gu) : 89.03774 89.49788 91.52993 assigned negative charge : -446.8035 centred at (gu) : 88.98001 89.32561 91.47234 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8078 nv = 96 ne = 84 npr = 62630 no. pairs analyzed = 62630 no. exposed pairs = 3460 no. arc points = 23996 no. surface atoms = 1165 nbur = 1822 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4646 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2422 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3776736E-09 1.7390176E-08 midg,1,midg; midg,igrid,midg -2.1922748E-08 2.5071959E-08 1,midg,midg; igrid,midg,midg -4.2746162E-09 1.0206439E-08 gauss-seidel spectral radius is 0.9874226 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 14:32:30 rms-change max change #iterations 0.1570096 21.43439 at 10iterations 1.5975352E-02 2.437195 at 20iterations 1.6121621E-03 0.2143326 at 30iterations 1.7882195E-04 2.3587227E-02 at 40iterations 2.2321516E-05 2.9582977E-03 at 50iterations finished qdiffx linear iterations at : 14:32:34 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 2.2321516E-05 2.9582977E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 14:32:35 4.557u 0.373s 0:05.29 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 Sat Oct 8 2011 at 14:32:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2987 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.923388 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): -11.49800 42.43500 ymin,ymax (A): -22.17400 22.64400 zmin,zma (A): -7.213000 48.31400 x,y,z range (A): 53.93300 44.81800 55.52700 scale (grids/A): 1.923388 object centre (A): 15.46850 0.2349997 20.55050 number of atom coordinates read : 2987 total number of charged atoms : 2842 net assigned charge : 3.000005 assigned positive charge : 449.8027 centred at (gu) : 87.11279 88.49306 94.58919 assigned negative charge : -446.8035 centred at (gu) : 86.93984 87.97658 94.41683 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23996 grid for indexing accessible points = 1.400000 m= 31928 mr = 63045 m= 4838 mr = 24035 m= 275 mr = 2918 m= 5 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 812 time to turn everything in is 0.7100000 number of dielectric boundary points 34915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22384 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) : 0.6411295 object centre at (A) : 15.46850 0.2349997 20.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3420282E-02 2.8700819E-02 midg,1,midg; midg,igrid,midg -5.7096868E-03 3.1225260E-02 1,midg,midg; igrid,midg,midg -3.8962867E-02 1.5708534E-02 gauss-seidel spectral radius is 0.9986915 estimated iterations to convergence 219 setup time was (sec) 1.070000 now iterating at: 14:32:36 rms-change max change #iterations 4.701708 212.1402 at 10iterations 2.252866 70.21534 at 20iterations 1.071409 32.61643 at 30iterations 0.5103629 14.97504 at 40iterations 0.2434108 7.081357 at 50iterations 0.1157395 3.376627 at 60iterations 5.5332333E-02 1.597090 at 70iterations 2.6328221E-02 0.7725201 at 80iterations 1.2581249E-02 0.3818703 at 90iterations 6.0074222E-03 0.1865540 at 100iterations 2.8543780E-03 8.9761734E-02 at 110iterations 1.3681282E-03 4.2710304E-02 at 120iterations finished qdiffx linear iterations at : 14:32:46 total time elapsed so far: 11.00000 # loops : 120 mean,max change (kT/e) : 1.3681282E-03 4.2710304E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.16000 DelPhi exited at 14:32:46 11.166u 0.427s 0:11.84 97.8% 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 14:32:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2987 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.885083 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): -11.49800 42.43500 ymin,ymax (A): -22.17400 22.64400 zmin,zma (A): -7.213000 48.31400 x,y,z range (A): 53.93300 44.81800 55.52700 scale (grids/A): 2.885083 object centre (A): 15.46850 0.2349997 20.55050 number of atom coordinates read : 2987 total number of charged atoms : 2842 net assigned charge : 3.000005 assigned positive charge : 449.8027 centred at (gu) : 85.66896 87.73956 96.88361 assigned negative charge : -446.8035 centred at (gu) : 85.40977 86.96481 96.62522 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 203557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23996 grid for indexing accessible points = 1.400000 m= 104399 mr = 152413 m= 37021 mr = 86774 m= 8554 mr = 29816 m= 1154 mr = 6277 m= 66 mr = 742 m= 0 mr = 18 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 2728 time to turn everything in is 1.850000 number of dielectric boundary points 78711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 22736 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) : 1.923388 object centre at (A) : 15.46850 0.2349997 20.55050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7894059E-02 0.3120157 midg,1,midg; midg,igrid,midg -2.2065397E-02 0.3362112 1,midg,midg; igrid,midg,midg -0.5362457 0.2070174 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 2.180000 now iterating at: 14:32:49 rms-change max change #iterations 10.88653 359.0267 at 10iterations 6.394191 131.1556 at 20iterations 3.724611 72.23768 at 30iterations 2.171839 43.25397 at 40iterations 1.261731 23.94288 at 50iterations 0.7338665 13.14705 at 60iterations 0.4258861 7.994275 at 70iterations 0.2462845 4.121658 at 80iterations 0.1424780 2.449017 at 90iterations 8.2656346E-02 1.391983 at 100iterations 4.7955636E-02 0.8509054 at 110iterations 2.7731376E-02 0.4586172 at 120iterations 1.6044140E-02 0.2563934 at 130iterations 9.3217362E-03 0.1680756 at 140iterations 5.3964383E-03 8.7951660E-02 at 150iterations 3.1287160E-03 5.1111698E-02 at 160iterations 1.8181354E-03 2.9191971E-02 at 170iterations 1.0608035E-03 1.9073486E-02 at 180iterations finished qdiffx linear iterations at : 14:33:05 total time elapsed so far: 18.25000 # loops : 180 mean,max change (kT/e) : 1.0608035E-03 1.9073486E-02 energy calculations done at 18.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.42000 DelPhi exited at 14:33:06 18.424u 0.454s 0:19.15 98.5% 0+0k 0+0io 0pf+0w