Tue Oct 11 05:28:39 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+sph2.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 = amb2.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 05:28:39 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.7396942 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 0.7396942 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 316.2980 centred at (gu) : 90.29611 89.77464 91.06687 assigned negative charge : -310.2591 centred at (gu) : 90.21365 89.69120 90.95203 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7725 nv = 96 ne = 84 npr = 40102 no. pairs analyzed = 40102 no. exposed pairs = 2497 no. arc points = 17124 no. surface atoms = 852 nbur = 1183 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4556 m= 4 mr = 127 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 0.2900000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1523 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8232 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4007963E-09 2.6319520E-07 midg,1,midg; midg,igrid,midg 2.2788093E-08 1.7778160E-07 1,midg,midg; igrid,midg,midg 2.2167587E-08 1.9482141E-07 gauss-seidel spectral radius is 0.9904623 estimated iterations to convergence 83 setup time was (sec) 0.5200000 now iterating at: 05:28:40 rms-change max change #iterations 0.2451494 46.19092 at 10iterations 3.3481508E-02 4.268242 at 20iterations 4.6738656E-03 0.7222042 at 30iterations 7.3682104E-04 9.2027426E-02 at 40iterations 1.6455373E-04 1.9966125E-02 at 50iterations finished qdiffx linear iterations at : 05:28:43 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.6455373E-04 1.9966125E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 05:28:43 3.359u 0.150s 0:03.82 91.6% 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 05:28:43 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.219083 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 2.219083 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 316.2980 centred at (gu) : 90.88830 89.32388 93.20069 assigned negative charge : -310.2591 centred at (gu) : 90.64111 89.07365 92.85618 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 34523 mr = 58012 m= 7511 mr = 26731 m= 777 mr = 5193 m= 43 mr = 436 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15404 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) : 0.7396942 object centre at (A) : 5.711000 9.512500 14.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1365316E-02 4.7167875E-02 midg,1,midg; midg,igrid,midg 3.0375294E-02 2.9677818E-02 1,midg,midg; igrid,midg,midg 4.0551174E-02 4.7763716E-02 gauss-seidel spectral radius is 0.9989132 estimated iterations to convergence 240 setup time was (sec) 0.9300000 now iterating at: 05:28:44 rms-change max change #iterations 4.985421 195.0994 at 10iterations 2.527270 80.92069 at 20iterations 1.287969 42.69099 at 30iterations 0.6554580 20.52308 at 40iterations 0.3336484 9.913013 at 50iterations 0.1701141 4.854126 at 60iterations 8.6512111E-02 2.907413 at 70iterations 4.4109829E-02 1.321956 at 80iterations 2.2550385E-02 0.6710172 at 90iterations 1.1577016E-02 0.3316593 at 100iterations 5.9834463E-03 0.1690149 at 110iterations 3.1301568E-03 9.2136383E-02 at 120iterations finished qdiffx linear iterations at : 05:28:51 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 3.1301568E-03 9.2136383E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 05:28:51 7.607u 0.171s 0:08.05 96.5% 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 Tue Oct 11 2011 at 05:28:51 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.328624 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 3.328624 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 316.2980 centred at (gu) : 91.33247 88.98579 94.80099 assigned negative charge : -310.2591 centred at (gu) : 90.96163 88.61040 94.28427 start vw surface at 0.1700000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 186368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 105328 mr = 139307 m= 45928 mr = 88469 m= 14145 mr = 38320 m= 3114 mr = 11237 m= 440 mr = 2324 m= 41 mr = 299 m= 0 mr = 17 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 75391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15472 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) : 2.219083 object centre at (A) : 5.711000 9.512500 14.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5366973 0.4496699 midg,1,midg; midg,igrid,midg 0.2571711 0.1344696 1,midg,midg; igrid,midg,midg 0.2259593 0.2772117 gauss-seidel spectral radius is 0.9993189 estimated iterations to convergence 302 setup time was (sec) 2.360000 now iterating at: 05:28:54 rms-change max change #iterations 10.91113 301.9970 at 10iterations 6.528714 146.9570 at 20iterations 3.887407 69.25979 at 30iterations 2.317403 43.14622 at 40iterations 1.377023 33.70650 at 50iterations 0.8170223 13.74783 at 60iterations 0.4839621 8.143938 at 70iterations 0.2866942 6.829312 at 80iterations 0.1698807 2.825013 at 90iterations 0.1005039 1.698769 at 100iterations 5.9725914E-02 1.166220 at 110iterations 3.5447229E-02 0.6332493 at 120iterations 2.1305120E-02 0.3673630 at 130iterations 1.2970817E-02 0.2088213 at 140iterations 8.1255436E-03 0.1581383 at 150iterations 5.3013894E-03 9.4486237E-02 at 160iterations 3.6420159E-03 7.3467255E-02 at 170iterations 2.6674287E-03 4.7046661E-02 at 180iterations finished qdiffx linear iterations at : 05:29:04 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 2.6674287E-03 4.7046661E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 05:29:05 12.834u 0.180s 0:13.46 96.6% 0+0k 0+0io 0pf+0w