Tue Oct 11 00:48:32 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 Tue Oct 11 2011 at 00:48:32 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 = 2714 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 0.5610275 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 0.5610275 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2569 net assigned charge : 4.228016 assigned positive charge : 408.2225 centred at (gu) : 92.61076 90.41943 89.88573 assigned negative charge : -403.9953 centred at (gu) : 92.38972 90.31452 90.07940 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 55176 no. pairs analyzed = 55176 no. exposed pairs = 3200 no. arc points = 22594 no. surface atoms = 1081 nbur = 1633 mkacc time = 0.1500000 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 = 1.540000 m= 208 mr = 3006 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2255 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4217952E-09 -1.6163643E-09 midg,1,midg; midg,igrid,midg -6.3677047E-10 1.6251698E-09 1,midg,midg; igrid,midg,midg -1.0349005E-09 5.0073545E-09 gauss-seidel spectral radius is 0.9835845 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 00:48:33 rms-change max change #iterations 8.2273252E-02 14.28215 at 10iterations 6.8446454E-03 1.253273 at 20iterations 1.0044380E-03 0.2638206 at 30iterations 2.4972271E-04 6.8420410E-02 at 40iterations 6.5786197E-05 1.8119812E-02 at 50iterations finished qdiffx linear iterations at : 00:48:36 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 6.5786197E-05 1.8119812E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 00:48:37 4.060u 0.262s 0:04.73 91.3% 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 Tue Oct 11 2011 at 00:48:37 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 = 2714 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 1.683082 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 1.683082 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2569 net assigned charge : 4.228016 assigned positive charge : 408.2225 centred at (gu) : 97.83167 91.25745 89.65634 assigned negative charge : -403.9953 centred at (gu) : 97.16889 90.94312 90.23811 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 19228 mr = 42914 m= 2113 mr = 13727 m= 69 mr = 1132 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1797 time to turn everything in is 0.5600000 number of dielectric boundary points 25100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19822 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) : 0.5610275 object centre at (A) : -5.313500 59.74750 14.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4601462E-02 -3.3652068E-03 midg,1,midg; midg,igrid,midg -4.9977470E-03 9.7093293E-03 1,midg,midg; igrid,midg,midg -3.4497335E-04 -8.1567634E-03 gauss-seidel spectral radius is 0.9982576 estimated iterations to convergence 190 setup time was (sec) 0.8400000 now iterating at: 00:48:38 rms-change max change #iterations 3.345206 164.1747 at 10iterations 1.410433 63.63840 at 20iterations 0.5995562 23.75138 at 30iterations 0.2550682 8.960911 at 40iterations 0.1086204 3.858826 at 50iterations 4.6313658E-02 1.689280 at 60iterations 1.9807890E-02 0.7468185 at 70iterations 8.5648093E-03 0.3104630 at 80iterations 3.7613967E-03 0.1428452 at 90iterations 1.7077104E-03 7.7861786E-02 at 100iterations 8.2978857E-04 3.9279938E-02 at 110iterations 4.2749659E-04 2.1520615E-02 at 120iterations finished qdiffx linear iterations at : 00:48:46 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 4.2749659E-04 2.1520615E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.100000 DelPhi exited at 00:48:47 9.103u 0.286s 0:10.44 89.8% 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 Tue Oct 11 2011 at 00:48:47 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 = 2714 !!! WARNING: ASP 298 has a net charge of -0.2720 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: 2.524624 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): -37.04100 26.41400 ymin,ymax (A): 32.59500 86.90000 zmin,zma (A): -7.287000 35.54500 x,y,z range (A): 63.45500 54.30500 42.83200 scale (grids/A): 2.524624 object centre (A): -5.313500 59.74750 14.12900 number of atom coordinates read : 2714 total number of charged atoms : 2569 net assigned charge : 4.228016 assigned positive charge : 408.2225 centred at (gu) : 101.7475 91.88614 89.48418 assigned negative charge : -403.9953 centred at (gu) : 100.7533 91.41448 90.35693 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 142937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 66633 mr = 104642 m= 19354 mr = 53872 m= 3345 mr = 15030 m= 255 mr = 2318 m= 2 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 5889 time to turn everything in is 1.310000 number of dielectric boundary points 56533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 20539 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) : 1.683082 object centre at (A) : -5.313500 59.74750 14.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1751312 -4.0864475E-02 midg,1,midg; midg,igrid,midg -0.1104298 7.9324268E-02 1,midg,midg; igrid,midg,midg 9.4188176E-02 -0.2282632 gauss-seidel spectral radius is 0.9991470 estimated iterations to convergence 270 setup time was (sec) 1.610000 now iterating at: 00:48:49 rms-change max change #iterations 8.383352 332.7074 at 10iterations 4.651337 128.2473 at 20iterations 2.581512 58.20611 at 30iterations 1.426937 28.19234 at 40iterations 0.7886785 16.00662 at 50iterations 0.4348941 9.211258 at 60iterations 0.2398032 5.324223 at 70iterations 0.1325625 3.204664 at 80iterations 7.3209196E-02 1.630792 at 90iterations 4.0406194E-02 0.8155365 at 100iterations 2.2374213E-02 0.4750671 at 110iterations 1.2453166E-02 0.2650242 at 120iterations 6.9806296E-03 0.1606827 at 130iterations 3.9579575E-03 0.1020660 at 140iterations 2.2936638E-03 5.9631348E-02 at 150iterations 1.3822006E-03 3.5316467E-02 at 160iterations 8.6723798E-04 2.6321411E-02 at 170iterations 5.7144184E-04 1.6990662E-02 at 180iterations finished qdiffx linear iterations at : 00:49:02 total time elapsed so far: 14.61000 # loops : 180 mean,max change (kT/e) : 5.7144184E-04 1.6990662E-02 energy calculations done at 14.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.79000 DelPhi exited at 00:49:03 14.791u 0.321s 0:15.39 98.1% 0+0k 0+0io 0pf+0w