Sun Oct 9 08:46:00 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 Sun Oct 9 2011 at 08:46:00 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 = 5330 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4910684 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 0.4910684 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.000040 assigned positive charge : 798.5488 centred at (gu) : 90.17258 88.70919 90.51005 assigned negative charge : -794.5550 centred at (gu) : 90.12555 88.77267 90.65335 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8197 nv = 96 ne = 84 npr = 105250 no. pairs analyzed = 105250 no. exposed pairs = 6839 no. arc points = 47725 no. surface atoms = 2295 nbur = 3035 mkacc time = 0.2300000 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 = 1.736000 m= 302 mr = 4091 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4602 ## 715 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6749827E-10 -1.7761159E-10 midg,1,midg; midg,igrid,midg 1.4139435E-10 -3.8030752E-11 1,midg,midg; igrid,midg,midg -3.2759136E-11 8.3170346E-11 gauss-seidel spectral radius is 0.9788494 estimated iterations to convergence 57 setup time was (sec) 0.6900000 now iterating at: 08:46:01 rms-change max change #iterations 5.8234215E-02 9.925682 at 10iterations 3.4423389E-03 0.5776863 at 20iterations 5.9661240E-04 0.1613083 at 30iterations 1.8416390E-04 4.9320221E-02 at 40iterations 6.0613551E-05 1.5625000E-02 at 50iterations finished qdiffx linear iterations at : 08:46:03 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.0613551E-05 1.5625000E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:46:04 3.352u 0.166s 0:03.86 90.9% 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 Sun Oct 9 2011 at 08:46:04 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 = 5330 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.473205 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 1.473205 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.000040 assigned positive charge : 798.5488 centred at (gu) : 90.51617 86.12601 91.52867 assigned negative charge : -794.5550 centred at (gu) : 90.37609 86.31783 91.95995 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 92428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47725 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26036 mr = 62023 m= 1928 mr = 16811 m= 34 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.6400000 number of dielectric boundary points 40873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 38239 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) : 0.4910684 object centre at (A) : 61.71350 54.15100 81.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6626274E-02 -4.2221164E-03 midg,1,midg; midg,igrid,midg -5.3956365E-04 -9.6225888E-03 1,midg,midg; igrid,midg,midg 8.4198704E-03 1.8915243E-02 gauss-seidel spectral radius is 0.9980047 estimated iterations to convergence 178 setup time was (sec) 0.9100000 now iterating at: 08:46:05 rms-change max change #iterations 3.657718 159.5405 at 10iterations 1.455374 50.65508 at 20iterations 0.5834998 20.79432 at 30iterations 0.2334006 7.768559 at 40iterations 9.3466580E-02 3.022557 at 50iterations 3.7412498E-02 1.262221 at 60iterations 1.4988620E-02 0.5385289 at 70iterations 6.1060400E-03 0.1921616 at 80iterations 2.5085374E-03 7.9910278E-02 at 90iterations 1.0654411E-03 3.8791656E-02 at 100iterations 4.8869569E-04 2.2182465E-02 at 110iterations 2.5015016E-04 1.1192322E-02 at 120iterations finished qdiffx linear iterations at : 08:46:11 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 2.5015016E-04 1.1192322E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 08:46:12 7.232u 0.196s 0:07.70 96.3% 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 Sun Oct 9 2011 at 08:46:12 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 = 5330 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.209808 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): 27.75000 95.67700 ymin,ymax (A): 21.84200 86.46000 zmin,zma (A): 45.41400 117.9090 x,y,z range (A): 67.92700 64.61800 72.49500 scale (grids/A): 2.209808 object centre (A): 61.71350 54.15100 81.66150 number of atom coordinates read : 5330 total number of charged atoms : 5168 net assigned charge : 4.000040 assigned positive charge : 798.5488 centred at (gu) : 90.77395 84.18861 92.29257 assigned negative charge : -794.5550 centred at (gu) : 90.56409 84.47675 92.93992 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 215428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47725 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 94062 mr = 152611 m= 22341 mr = 72328 m= 2554 mr = 15712 m= 80 mr = 1421 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 2809 time to turn everything in is 1.510000 number of dielectric boundary points 92383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 41157 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) : 1.473205 object centre at (A) : 61.71350 54.15100 81.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2809354 8.0110870E-02 midg,1,midg; midg,igrid,midg 1.0723815E-02 -0.2281709 1,midg,midg; igrid,midg,midg 0.1325301 0.3912183 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.810000 now iterating at: 08:46:14 rms-change max change #iterations 10.35475 318.1375 at 10iterations 5.943993 142.2197 at 20iterations 3.397041 72.85173 at 30iterations 1.931499 41.80520 at 40iterations 1.090465 24.32618 at 50iterations 0.6135153 13.62961 at 60iterations 0.3450884 6.961527 at 70iterations 0.1928954 4.231899 at 80iterations 0.1079980 2.044640 at 90iterations 6.0206886E-02 1.212295 at 100iterations 3.3562776E-02 0.7352066 at 110iterations 1.8684478E-02 0.3606930 at 120iterations 1.0421171E-02 0.1949358 at 130iterations 5.7879714E-03 0.1320591 at 140iterations 3.2282011E-03 6.0193419E-02 at 150iterations 1.8048706E-03 3.5408020E-02 at 160iterations 1.0116093E-03 2.1766663E-02 at 170iterations 5.7063933E-04 1.0223389E-02 at 180iterations finished qdiffx linear iterations at : 08:46:24 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 5.7063933E-04 1.0223389E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 08:46:25 12.477u 0.191s 0:12.98 97.5% 0+0k 0+0io 0pf+0w