Mon Oct 10 10:23:46 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 Mon Oct 10 2011 at 10:23:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 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: 0.5676382 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 0.5676382 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.00003 assigned positive charge : 397.0502 centred at (gu) : 92.07827 91.05862 86.71661 assigned negative charge : -387.0505 centred at (gu) : 92.14698 91.07757 86.56441 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5798 nv = 96 ne = 84 npr = 52900 no. pairs analyzed = 52900 no. exposed pairs = 3968 no. arc points = 28719 no. surface atoms = 1324 nbur = 1384 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 = 1.512000 m= 233 mr = 2554 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1121724E-09 1.5412548E-09 midg,1,midg; midg,igrid,midg 1.3352367E-09 1.5837647E-09 1,midg,midg; igrid,midg,midg 1.4258053E-09 9.7669905E-10 gauss-seidel spectral radius is 0.9839777 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 10:23:47 rms-change max change #iterations 8.3164550E-02 15.13141 at 10iterations 5.9930393E-03 1.114554 at 20iterations 4.6013284E-04 8.6640358E-02 at 30iterations 3.7424623E-05 6.9127083E-03 at 40iterations 4.0962937E-06 5.4550171E-04 at 50iterations finished qdiffx linear iterations at : 10:23:50 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.0962937E-06 5.4550171E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:23:50 3.454u 0.163s 0:04.02 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 Mon Oct 10 2011 at 10:23:50 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 = 2708 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: 1.702915 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 1.702915 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.00003 assigned positive charge : 397.0502 centred at (gu) : 96.23456 93.17541 80.14951 assigned negative charge : -387.0505 centred at (gu) : 96.44084 93.23251 79.69304 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28719 grid for indexing accessible points = 1.400000 m= 18814 mr = 37988 m= 2191 mr = 11988 m= 68 mr = 980 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 32124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19817 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) : 0.5676382 object centre at (A) : 9.200001 16.29950 25.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5156443E-03 8.2317144E-03 midg,1,midg; midg,igrid,midg 1.7894998E-02 1.8800067E-02 1,midg,midg; igrid,midg,midg -1.6476903E-02 1.7007889E-02 gauss-seidel spectral radius is 0.9983112 estimated iterations to convergence 193 setup time was (sec) 0.5500000 now iterating at: 10:23:51 rms-change max change #iterations 3.341419 175.2706 at 10iterations 1.423873 53.37016 at 20iterations 0.6100189 26.07628 at 30iterations 0.2605546 10.12164 at 40iterations 0.1118067 4.114994 at 50iterations 4.7781013E-02 1.792755 at 60iterations 2.0413846E-02 0.7862892 at 70iterations 8.7740654E-03 0.3956718 at 80iterations 3.7601194E-03 0.1524504 at 90iterations 1.6124620E-03 6.1920166E-02 at 100iterations 6.9283519E-04 2.8980255E-02 at 110iterations 2.9805102E-04 1.0793686E-02 at 120iterations finished qdiffx linear iterations at : 10:23:58 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.9805102E-04 1.0793686E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 10:23:59 7.823u 0.188s 0:08.37 95.5% 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 10:23:59 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 = 2708 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: 2.554372 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 2.554372 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.00003 assigned positive charge : 397.0502 centred at (gu) : 99.35160 94.76308 75.22428 assigned negative charge : -387.0505 centred at (gu) : 99.66120 94.84869 74.53951 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28719 grid for indexing accessible points = 1.400000 m= 63149 mr = 94047 m= 19286 mr = 47196 m= 3403 mr = 13739 m= 259 mr = 2070 m= 6 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 72491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20486 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) : 1.702915 object centre at (A) : 9.200001 16.29950 25.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1100454 8.6923309E-02 midg,1,midg; midg,igrid,midg 0.3244119 0.2451416 1,midg,midg; igrid,midg,midg -0.6780891 0.2664760 gauss-seidel spectral radius is 0.9991748 estimated iterations to convergence 275 setup time was (sec) 1.020000 now iterating at: 10:24:00 rms-change max change #iterations 8.710928 336.8942 at 10iterations 5.029920 136.4545 at 20iterations 2.885093 78.14626 at 30iterations 1.636474 49.42496 at 40iterations 0.9249240 27.37344 at 50iterations 0.5198750 14.16449 at 60iterations 0.2917381 7.545873 at 70iterations 0.1637987 3.911991 at 80iterations 9.1383271E-02 1.973007 at 90iterations 5.1102642E-02 1.113609 at 100iterations 2.8519634E-02 0.6520433 at 110iterations 1.5927475E-02 0.3734579 at 120iterations 8.8885212E-03 0.2014627 at 130iterations 4.9522705E-03 0.1138172 at 140iterations 2.7537218E-03 6.0447693E-02 at 150iterations 1.5358686E-03 3.1428158E-02 at 160iterations 8.5292949E-04 1.8723965E-02 at 170iterations 4.7607048E-04 1.0027885E-02 at 180iterations finished qdiffx linear iterations at : 10:24:11 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 4.7607048E-04 1.0027885E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 10:24:12 12.503u 0.200s 0:12.97 97.9% 0+0k 0+0io 0pf+0w