Sun Oct 9 15:23:09 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 15:23:09 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 = 5365 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: 0.5009288 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 0.5009288 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 817.7023 centred at (gu) : 89.07073 90.59291 90.50888 assigned negative charge : -819.2092 centred at (gu) : 89.09180 90.52331 90.57926 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8186 nv = 96 ne = 84 npr = 111282 no. pairs analyzed = 111282 no. exposed pairs = 6017 no. arc points = 42089 no. surface atoms = 2019 nbur = 3346 mkacc time = 0.1900000 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 = 1.708000 m= 269 mr = 4490 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3600000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4021 ## 592 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11205 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0598996E-10 -1.7550937E-10 midg,1,midg; midg,igrid,midg -1.2883949E-10 1.4154955E-10 1,midg,midg; igrid,midg,midg 3.4746990E-11 -4.3199853E-11 gauss-seidel spectral radius is 0.9796518 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:23:10 rms-change max change #iterations 6.5974325E-02 11.04329 at 10iterations 3.9978763E-03 0.6059923 at 20iterations 4.7466904E-04 7.0625305E-02 at 30iterations 1.0331927E-04 1.7724991E-02 at 40iterations 2.4584628E-05 4.3144226E-03 at 50iterations finished qdiffx linear iterations at : 15:23:13 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.4584628E-05 4.3144226E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:23:13 3.615u 0.174s 0:04.13 91.5% 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 Sun Oct 9 2011 at 15:23:13 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 = 5365 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: 1.502786 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 1.502786 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 817.7023 centred at (gu) : 87.21082 91.77747 91.52533 assigned negative charge : -819.2092 centred at (gu) : 87.27518 91.56960 91.73768 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 94496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 26597 mr = 67295 m= 2233 mr = 18234 m= 48 mr = 1027 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 5798 time to turn everything in is 0.4700000 number of dielectric boundary points 36816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 38797 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) : 0.5009288 object centre at (A) : 103.0030 25.45850 30.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9743064E-04 -4.9203732E-03 midg,1,midg; midg,igrid,midg -7.7619781E-03 8.8229626E-03 1,midg,midg; igrid,midg,midg -1.8242773E-02 7.5337198E-03 gauss-seidel spectral radius is 0.9980676 estimated iterations to convergence 181 setup time was (sec) 0.6900000 now iterating at: 15:23:14 rms-change max change #iterations 3.924767 154.4000 at 10iterations 1.588352 53.12813 at 20iterations 0.6455744 19.51855 at 30iterations 0.2612559 8.750836 at 40iterations 0.1066934 3.382492 at 50iterations 4.3451097E-02 1.310884 at 60iterations 1.7719757E-02 0.5533028 at 70iterations 7.2093643E-03 0.2281532 at 80iterations 2.9589501E-03 9.7993851E-02 at 90iterations 1.2079509E-03 3.6766648E-02 at 100iterations 4.9806683E-04 1.5243530E-02 at 110iterations 2.0808786E-04 6.8893433E-03 at 120iterations finished qdiffx linear iterations at : 15:23:21 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.0808786E-04 6.8893433E-03 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 15:23:22 7.963u 0.181s 0:08.46 96.2% 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 15:23:22 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 = 5365 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: 2.254179 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 2.254179 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 817.7023 centred at (gu) : 85.81564 92.66582 92.28752 assigned negative charge : -819.2092 centred at (gu) : 85.91277 92.35458 92.60618 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 220967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 96964 mr = 165012 m= 23917 mr = 77335 m= 3176 mr = 17630 m= 133 mr = 2011 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 19241 time to turn everything in is 1.080000 number of dielectric boundary points 83122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 41449 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) : 1.502786 object centre at (A) : 103.0030 25.45850 30.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3838546E-03 -0.1043726 midg,1,midg; midg,igrid,midg -0.1725736 0.2152611 1,midg,midg; igrid,midg,midg -0.5372953 0.3385067 gauss-seidel spectral radius is 0.9991526 estimated iterations to convergence 271 setup time was (sec) 1.340000 now iterating at: 15:23:23 rms-change max change #iterations 10.52467 299.3618 at 10iterations 5.926577 120.4400 at 20iterations 3.323943 85.63628 at 30iterations 1.852310 37.06156 at 40iterations 1.030947 20.92604 at 50iterations 0.5740686 10.55005 at 60iterations 0.3179614 6.047470 at 70iterations 0.1764711 3.031710 at 80iterations 9.7849615E-02 1.995966 at 90iterations 5.4263275E-02 0.9558678 at 100iterations 2.9946499E-02 0.5663681 at 110iterations 1.6587807E-02 0.2810936 at 120iterations 9.1838129E-03 0.1710930 at 130iterations 5.0679939E-03 8.5462570E-02 at 140iterations 2.8116666E-03 5.1136494E-02 at 150iterations 1.5554960E-03 2.5409698E-02 at 160iterations 8.6147955E-04 1.6151428E-02 at 170iterations 4.7647432E-04 9.3116760E-03 at 180iterations finished qdiffx linear iterations at : 15:23:35 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 4.7647432E-04 9.3116760E-03 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 15:23:35 13.056u 0.205s 0:13.54 97.8% 0+0k 0+0io 0pf+0w