Tue Oct 11 08:33:49 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 08:33:49 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7165285 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 0.7165285 object centre (A): 2.821500 7.420500 21.37300 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 319.1341 centred at (gu) : 89.57275 90.11580 90.74967 assigned negative charge : -313.2031 centred at (gu) : 89.43706 90.12473 90.80489 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6823 nv = 96 ne = 84 npr = 44044 no. pairs analyzed = 44044 no. exposed pairs = 2352 no. arc points = 16046 no. surface atoms = 809 nbur = 1280 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3954 m= 3 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1508 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7905 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3221735E-08 3.2943984E-08 midg,1,midg; midg,igrid,midg 6.6556524E-08 5.8414905E-08 1,midg,midg; igrid,midg,midg -2.2937629E-08 1.3243698E-07 gauss-seidel spectral radius is 0.9898369 estimated iterations to convergence 81 setup time was (sec) 0.6000000 now iterating at: 08:33:49 rms-change max change #iterations 0.2188849 30.65790 at 10iterations 2.7683847E-02 3.720736 at 20iterations 3.5309207E-03 0.5493441 at 30iterations 4.6233099E-04 6.8412781E-02 at 40iterations 6.3283012E-05 9.3841553E-03 at 50iterations finished qdiffx linear iterations at : 08:33:53 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 6.3283012E-05 9.3841553E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 08:33:53 4.183u 0.281s 0:04.92 90.6% 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 08:33:54 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.149585 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 2.149585 object centre (A): 2.821500 7.420500 21.37300 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 319.1341 centred at (gu) : 88.71818 90.34744 92.24901 assigned negative charge : -313.2031 centred at (gu) : 88.31124 90.37424 92.41479 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16046 grid for indexing accessible points = 1.400000 m= 27038 mr = 52738 m= 4878 mr = 20146 m= 401 mr = 3061 m= 8 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 29779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15545 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) : 0.7165285 object centre at (A) : 2.821500 7.420500 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8473915E-02 6.9968626E-02 midg,1,midg; midg,igrid,midg 2.6316594E-02 4.4144350E-03 1,midg,midg; igrid,midg,midg -6.7252778E-03 3.3844929E-02 gauss-seidel spectral radius is 0.9988475 estimated iterations to convergence 233 setup time was (sec) 0.9800000 now iterating at: 08:33:55 rms-change max change #iterations 4.770210 175.4720 at 10iterations 2.363678 69.71127 at 20iterations 1.176730 36.77223 at 30iterations 0.5886612 17.24563 at 40iterations 0.2926911 8.922442 at 50iterations 0.1464700 4.194098 at 60iterations 7.3249273E-02 2.320916 at 70iterations 3.6480937E-02 1.127571 at 80iterations 1.8199481E-02 0.5151882 at 90iterations 9.1120256E-03 0.2859502 at 100iterations 4.5448784E-03 0.1420794 at 110iterations 2.2767205E-03 7.3339462E-02 at 120iterations finished qdiffx linear iterations at : 08:34:03 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 2.2767205E-03 7.3339462E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 08:34:04 9.794u 0.339s 0:10.48 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 08:34:04 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.224378 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 3.224378 object centre (A): 2.821500 7.420500 21.37300 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 319.1341 centred at (gu) : 88.07742 90.52119 93.37345 assigned negative charge : -313.2031 centred at (gu) : 87.46688 90.56143 93.62212 start vw surface at 0.1500000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 170249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16046 grid for indexing accessible points = 1.400000 m= 87182 mr = 127291 m= 32897 mr = 71985 m= 8998 mr = 26631 m= 1641 mr = 6749 m= 169 mr = 1116 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.160000 number of dielectric boundary points 67276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15640 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) : 2.149585 object centre at (A) : 2.821500 7.420500 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2279603 0.7132261 midg,1,midg; midg,igrid,midg 0.2098759 -2.2929588E-02 1,midg,midg; igrid,midg,midg 6.0493522E-03 0.2982189 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.490000 now iterating at: 08:34:07 rms-change max change #iterations 10.51439 333.1466 at 10iterations 6.204596 128.9447 at 20iterations 3.638768 67.92772 at 30iterations 2.141057 37.06929 at 40iterations 1.253092 23.87329 at 50iterations 0.7356903 16.94891 at 60iterations 0.4293808 7.943658 at 70iterations 0.2512005 5.285152 at 80iterations 0.1471202 2.457619 at 90iterations 8.6123064E-02 1.493570 at 100iterations 5.0278042E-02 0.8212070 at 110iterations 2.9434571E-02 0.5224934 at 120iterations 1.7258136E-02 0.3009186 at 130iterations 1.0141734E-02 0.1874294 at 140iterations 6.0312394E-03 0.1156139 at 150iterations 3.6094710E-03 6.2290192E-02 at 160iterations 2.2048415E-03 3.8288116E-02 at 170iterations 1.3873723E-03 2.4732590E-02 at 180iterations finished qdiffx linear iterations at : 08:34:21 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 1.3873723E-03 2.4732590E-02 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 08:34:22 16.959u 0.339s 0:17.77 97.2% 0+0k 0+0io 0pf+0w