Tue Oct 11 03:25:05 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 03:25:05 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 = 2289 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6141531 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): -16.93900 32.89100 ymin,ymax (A): -20.83900 21.22800 zmin,zma (A): -7.057000 50.90900 x,y,z range (A): 49.83000 42.06700 57.96600 scale (grids/A): 0.6141531 object centre (A): 7.976000 0.1944990 21.92600 number of atom coordinates read : 2289 total number of charged atoms : 2144 net assigned charge : 2.000006 assigned positive charge : 332.5673 centred at (gu) : 91.68787 89.94444 89.12796 assigned negative charge : -330.5678 centred at (gu) : 91.69701 89.87582 89.24799 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5746 nv = 96 ne = 84 npr = 46767 no. pairs analyzed = 46767 no. exposed pairs = 2889 no. arc points = 21086 no. surface atoms = 975 nbur = 1314 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 266 mr = 2991 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2700000 number of dielectric boundary points 2998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2040 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7071 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4309999E-09 -3.6732057E-09 midg,1,midg; midg,igrid,midg -2.0147464E-09 4.4794191E-09 1,midg,midg; igrid,midg,midg 1.2048413E-09 1.2318468E-09 gauss-seidel spectral radius is 0.9862499 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 03:25:05 rms-change max change #iterations 0.1107387 19.10672 at 10iterations 9.7859288E-03 1.413352 at 20iterations 8.9581998E-04 0.1298885 at 30iterations 8.2047831E-05 1.3160706E-02 at 40iterations 8.3076275E-06 1.4724731E-03 at 50iterations finished qdiffx linear iterations at : 03:25:08 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 8.3076275E-06 1.4724731E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:25:09 3.322u 0.162s 0:04.03 86.3% 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 03:25:09 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 = 2289 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.842460 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): -16.93900 32.89100 ymin,ymax (A): -20.83900 21.22800 zmin,zma (A): -7.057000 50.90900 x,y,z range (A): 49.83000 42.06700 57.96600 scale (grids/A): 1.842460 object centre (A): 7.976000 0.1944990 21.92600 number of atom coordinates read : 2289 total number of charged atoms : 2144 net assigned charge : 2.000006 assigned positive charge : 332.5673 centred at (gu) : 95.06318 89.83296 87.38353 assigned negative charge : -330.5678 centred at (gu) : 95.09080 89.62740 87.74409 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21086 grid for indexing accessible points = 1.400000 m= 21270 mr = 41567 m= 3135 mr = 15262 m= 145 mr = 1880 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 841 time to turn everything in is 0.4500000 number of dielectric boundary points 27762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 16774 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) : 0.6141531 object centre at (A) : 7.976000 0.1944990 21.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1885160E-03 -3.9548062E-02 midg,1,midg; midg,igrid,midg -8.5101597E-04 1.1853971E-02 1,midg,midg; igrid,midg,midg 9.3156649E-03 4.6704514E-03 gauss-seidel spectral radius is 0.9985123 estimated iterations to convergence 206 setup time was (sec) 0.7100000 now iterating at: 03:25:10 rms-change max change #iterations 3.628158 186.4336 at 10iterations 1.635929 59.11776 at 20iterations 0.7408618 28.19782 at 30iterations 0.3338098 11.49913 at 40iterations 0.1523241 5.468540 at 50iterations 6.8770923E-02 2.397354 at 60iterations 3.1169010E-02 1.100655 at 70iterations 1.4057490E-02 0.4947224 at 80iterations 6.3813329E-03 0.2291965 at 90iterations 2.8943554E-03 0.1036224 at 100iterations 1.3128421E-03 4.4044495E-02 at 110iterations 5.9643708E-04 2.2639275E-02 at 120iterations finished qdiffx linear iterations at : 03:25:15 total time elapsed so far: 6.530000 # loops : 120 mean,max change (kT/e) : 5.9643708E-04 2.2639275E-02 energy calculations done at 6.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.700000 DelPhi exited at 03:25:16 6.703u 0.176s 0:07.39 92.9% 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 03:25:16 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 = 2289 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: 2.763689 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): -16.93900 32.89100 ymin,ymax (A): -20.83900 21.22800 zmin,zma (A): -7.057000 50.90900 x,y,z range (A): 49.83000 42.06700 57.96600 scale (grids/A): 2.763689 object centre (A): 7.976000 0.1944990 21.92600 number of atom coordinates read : 2289 total number of charged atoms : 2144 net assigned charge : 2.000006 assigned positive charge : 332.5673 centred at (gu) : 97.59460 89.74938 86.07522 assigned negative charge : -330.5678 centred at (gu) : 97.63612 89.44106 86.61615 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 143697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21086 grid for indexing accessible points = 1.400000 m= 69132 mr = 101412 m= 24470 mr = 55664 m= 5598 mr = 19348 m= 619 mr = 4090 m= 18 mr = 321 m= 0 mr = 4 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 2741 time to turn everything in is 1.080000 number of dielectric boundary points 62695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 17148 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) : 1.842460 object centre at (A) : 7.976000 0.1944990 21.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8008965E-02 -0.8255538 midg,1,midg; midg,igrid,midg 1.3356082E-02 0.1227038 1,midg,midg; igrid,midg,midg 0.1111855 3.5377596E-02 gauss-seidel spectral radius is 0.9992221 estimated iterations to convergence 283 setup time was (sec) 1.360000 now iterating at: 03:25:18 rms-change max change #iterations 8.707603 275.7172 at 10iterations 5.038063 153.2861 at 20iterations 2.891866 64.83551 at 30iterations 1.647010 41.34348 at 40iterations 0.9429173 20.22673 at 50iterations 0.5379748 11.95010 at 60iterations 0.3050460 7.271550 at 70iterations 0.1732220 4.437613 at 80iterations 9.8512895E-02 2.128130 at 90iterations 5.5886205E-02 1.317720 at 100iterations 3.1588633E-02 0.6864023 at 110iterations 1.7939648E-02 0.3695145 at 120iterations 1.0171295E-02 0.2020950 at 130iterations 5.7702246E-03 0.1296387 at 140iterations 3.2686684E-03 6.3506126E-02 at 150iterations 1.8549900E-03 3.9556503E-02 at 160iterations 1.0526400E-03 2.1236420E-02 at 170iterations 6.0089538E-04 1.2645245E-02 at 180iterations finished qdiffx linear iterations at : 03:25:27 total time elapsed so far: 10.53000 # loops : 180 mean,max change (kT/e) : 6.0089538E-04 1.2645245E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 03:25:27 10.710u 0.158s 0:11.19 97.0% 0+0k 0+0io 0pf+0w