Sun Oct 9 16:09:39 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+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 16:09:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 !!! WARNING: MG4 470 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5974057 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 0.5974057 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3019 net assigned charge : -5.099975 assigned positive charge : 469.7549 centred at (gu) : 89.93813 89.06516 91.83719 assigned negative charge : -474.8563 centred at (gu) : 89.95100 88.97791 91.86862 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7313 nv = 96 ne = 84 npr = 65711 no. pairs analyzed = 65711 no. exposed pairs = 3812 no. arc points = 26570 no. surface atoms = 1280 nbur = 1883 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 4022 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2200000 number of dielectric boundary points 3630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2655 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9334 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5386689E-10 -4.8984306E-09 midg,1,midg; midg,igrid,midg -6.8699504E-09 1.2774725E-09 1,midg,midg; igrid,midg,midg -1.4252552E-09 -2.4269202E-09 gauss-seidel spectral radius is 0.9855437 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 16:09:40 rms-change max change #iterations 0.1191813 17.55411 at 10iterations 9.9598635E-03 1.369240 at 20iterations 8.3655491E-04 0.1238832 at 30iterations 7.6939839E-05 1.1722565E-02 at 40iterations 1.1818963E-05 2.3880005E-03 at 50iterations finished qdiffx linear iterations at : 16:09:43 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1818963E-05 2.3880005E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 16:09:43 3.415u 0.187s 0:03.89 92.2% 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 16:09:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3163 !!! WARNING: MG4 470 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.792217 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 1.792217 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3019 net assigned charge : -5.099975 assigned positive charge : 469.7549 centred at (gu) : 89.81367 87.19427 95.51085 assigned negative charge : -474.8563 centred at (gu) : 89.85268 86.93340 95.60564 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26570 grid for indexing accessible points = 1.400000 m= 27480 mr = 56535 m= 4136 mr = 19816 m= 195 mr = 2512 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1160 time to turn everything in is 0.3800000 number of dielectric boundary points 33694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23522 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) : 0.5974057 object centre at (A) : 11.26450 -30.05900 22.56850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7756131E-03 7.6329643E-03 midg,1,midg; midg,igrid,midg -1.7148124E-02 -1.2488132E-02 1,midg,midg; igrid,midg,midg -3.0837955E-02 -2.0119596E-02 gauss-seidel spectral radius is 0.9985088 estimated iterations to convergence 205 setup time was (sec) 0.6100000 now iterating at: 16:09:44 rms-change max change #iterations 4.212021 174.6155 at 10iterations 1.901842 72.61663 at 20iterations 0.8583105 29.37308 at 30iterations 0.3892142 12.14922 at 40iterations 0.1756484 5.254103 at 50iterations 7.9730436E-02 2.723916 at 60iterations 3.5992432E-02 1.155003 at 70iterations 1.6332315E-02 0.4964199 at 80iterations 7.4030496E-03 0.2238064 at 90iterations 3.3543184E-03 0.1034603 at 100iterations 1.5202564E-03 4.6890974E-02 at 110iterations 6.8822433E-04 2.1415710E-02 at 120iterations finished qdiffx linear iterations at : 16:09:51 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 6.8822433E-04 2.1415710E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 16:09:52 7.968u 0.214s 0:08.44 96.8% 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 Sun Oct 9 2011 at 16:09:52 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 = 3163 !!! WARNING: MG4 470 has a net charge of 1.4000 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: 2.688325 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): -15.18500 37.71400 ymin,ymax (A): -56.13900 -3.979000 zmin,zma (A): -7.227000 52.36400 x,y,z range (A): 52.89900 52.16000 59.59100 scale (grids/A): 2.688325 object centre (A): 11.26450 -30.05900 22.56850 number of atom coordinates read : 3163 total number of charged atoms : 3019 net assigned charge : -5.099975 assigned positive charge : 469.7549 centred at (gu) : 89.72027 85.79122 98.26607 assigned negative charge : -474.8563 centred at (gu) : 89.77880 85.40011 98.40842 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 187616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26570 grid for indexing accessible points = 1.400000 m= 91060 mr = 137953 m= 31218 mr = 73529 m= 7099 mr = 24501 m= 861 mr = 5310 m= 36 mr = 548 m= 0 mr = 13 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3516 time to turn everything in is 1.010000 number of dielectric boundary points 76036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 24149 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) : 1.792217 object centre at (A) : 11.26450 -30.05900 22.56850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1622704 0.1104069 midg,1,midg; midg,igrid,midg -0.1642859 -0.1939263 1,midg,midg; igrid,midg,midg -0.4921295 -0.2538231 gauss-seidel spectral radius is 0.9992354 estimated iterations to convergence 285 setup time was (sec) 1.250000 now iterating at: 16:09:53 rms-change max change #iterations 10.18260 301.2607 at 10iterations 5.903716 138.4604 at 20iterations 3.401928 73.44901 at 30iterations 1.950895 44.08118 at 40iterations 1.122565 25.33015 at 50iterations 0.6416821 13.68034 at 60iterations 0.3679914 6.958399 at 70iterations 0.2100629 3.939209 at 80iterations 0.1198836 2.179017 at 90iterations 6.8331145E-02 1.254629 at 100iterations 3.8992271E-02 0.6825571 at 110iterations 2.2207424E-02 0.4054728 at 120iterations 1.2677087E-02 0.2190706 at 130iterations 7.2197774E-03 0.1280336 at 140iterations 4.1144793E-03 7.3229790E-02 at 150iterations 2.3421305E-03 4.0328503E-02 at 160iterations 1.3376687E-03 2.5539398E-02 at 170iterations 7.6408649E-04 1.4263153E-02 at 180iterations finished qdiffx linear iterations at : 16:10:04 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 7.6408649E-04 1.4263153E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 16:10:05 12.674u 0.212s 0:13.15 97.9% 0+0k 0+0io 0pf+0w