Sun Oct 9 00:50:59 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 00:50:59 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 = 2224 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: 0.6668790 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 0.6668790 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.1526 centred at (gu) : 90.23202 89.28828 88.81255 assigned negative charge : -314.1532 centred at (gu) : 90.24391 89.35401 88.86388 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6824 nv = 96 ne = 84 npr = 43920 no. pairs analyzed = 43920 no. exposed pairs = 3073 no. arc points = 22041 no. surface atoms = 1027 nbur = 1197 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3498 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7831 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4782895E-08 1.8716740E-08 midg,1,midg; midg,igrid,midg 5.2872917E-08 1.8111271E-08 1,midg,midg; igrid,midg,midg 3.3998269E-08 3.2535930E-08 gauss-seidel spectral radius is 0.9883199 estimated iterations to convergence 76 setup time was (sec) 0.5000000 now iterating at: 00:51:00 rms-change max change #iterations 0.1552010 26.48784 at 10iterations 1.6860578E-02 2.441537 at 20iterations 2.0079021E-03 0.2985065 at 30iterations 3.9360911E-04 5.5322647E-02 at 40iterations 1.3179342E-04 2.0780563E-02 at 50iterations finished qdiffx linear iterations at : 00:51:02 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.3179342E-04 2.0780563E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 00:51:03 3.275u 0.213s 0:03.78 92.0% 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 00:51:03 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 = 2224 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: 2.000637 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 2.000637 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.1526 centred at (gu) : 90.69584 87.86450 86.43739 assigned negative charge : -314.1532 centred at (gu) : 90.73192 88.06213 86.59175 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22041 grid for indexing accessible points = 1.400000 m= 27073 mr = 47851 m= 5135 mr = 19136 m= 440 mr = 3191 m= 13 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 34418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 16516 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) : 0.6668790 object centre at (A) : 26.44050 5.686500 58.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4085713E-02 4.9287785E-02 midg,1,midg; midg,igrid,midg 3.7694309E-02 4.6394286E-03 1,midg,midg; igrid,midg,midg 5.2094497E-02 5.2807268E-02 gauss-seidel spectral radius is 0.9987329 estimated iterations to convergence 223 setup time was (sec) 0.8500000 now iterating at: 00:51:04 rms-change max change #iterations 4.154613 230.4339 at 10iterations 1.993573 69.10852 at 20iterations 0.9563400 32.21519 at 30iterations 0.4593567 14.58023 at 40iterations 0.2198701 6.588926 at 50iterations 0.1058731 3.495163 at 60iterations 5.1078621E-02 1.547455 at 70iterations 2.4620479E-02 0.8328247 at 80iterations 1.1892966E-02 0.3967886 at 90iterations 5.7924725E-03 0.1806774 at 100iterations 2.8720773E-03 9.6263885E-02 at 110iterations 1.4676973E-03 4.8679352E-02 at 120iterations finished qdiffx linear iterations at : 00:51:10 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 1.4676973E-03 4.8679352E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 00:51:11 7.511u 0.208s 0:08.04 95.8% 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 00:51:11 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 = 2224 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: 3.000955 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 3.000955 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.1526 centred at (gu) : 91.04359 86.79655 84.65591 assigned negative charge : -314.1532 centred at (gu) : 91.09794 87.09325 84.88750 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 166401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22041 grid for indexing accessible points = 1.400000 m= 84521 mr = 116504 m= 33234 mr = 67239 m= 9573 mr = 26108 m= 1825 mr = 6989 m= 142 mr = 1202 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 77602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 16712 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) : 2.000637 object centre at (A) : 26.44050 5.686500 58.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3028811 0.6216483 midg,1,midg; midg,igrid,midg 0.3285320 2.5177678E-02 1,midg,midg; igrid,midg,midg 0.4563177 0.4440860 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 1.680000 now iterating at: 00:51:13 rms-change max change #iterations 9.776020 431.3605 at 10iterations 5.848146 148.6170 at 20iterations 3.471609 72.24525 at 30iterations 2.056726 43.32904 at 40iterations 1.213803 25.69056 at 50iterations 0.7118382 13.39475 at 60iterations 0.4184770 8.685838 at 70iterations 0.2445754 4.990891 at 80iterations 0.1433692 3.028565 at 90iterations 8.3929203E-02 1.898643 at 100iterations 4.9013291E-02 0.9911127 at 110iterations 2.8606521E-02 0.5306072 at 120iterations 1.6703131E-02 0.3207722 at 130iterations 9.7865118E-03 0.1729050 at 140iterations 5.7446784E-03 0.1073213 at 150iterations 3.3970047E-03 6.7223549E-02 at 160iterations 2.0422845E-03 4.1353226E-02 at 170iterations 1.2661114E-03 2.6168823E-02 at 180iterations finished qdiffx linear iterations at : 00:51:23 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 1.2661114E-03 2.6168823E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 00:51:24 12.418u 0.245s 0:12.93 97.8% 0+0k 0+0io 0pf+0w