Sun Oct 9 15:27:32 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 Sun Oct 9 2011 at 15:27:32 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5487 !!! WARNING: GLM 113 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4964994 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): 24.64800 85.15400 ymin,ymax (A): 11.29600 82.99800 zmin,zma (A): -36.05200 35.17100 x,y,z range (A): 60.50600 71.70200 71.22300 scale (grids/A): 0.4964994 object centre (A): 54.90100 47.14700 -0.4404984 number of atom coordinates read : 5487 total number of charged atoms : 5309 net assigned charge : -6.093958 assigned positive charge : 845.9523 centred at (gu) : 90.51643 90.97598 91.10990 assigned negative charge : -852.0540 centred at (gu) : 90.47279 90.95548 91.14360 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8116 nv = 96 ne = 84 npr = 111909 no. pairs analyzed = 111909 no. exposed pairs = 6663 no. arc points = 45430 no. surface atoms = 2240 nbur = 3247 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= 314 mr = 4249 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4255 ## 643 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2589634E-12 -1.3719989E-10 midg,1,midg; midg,igrid,midg -6.1256826E-11 -1.4185104E-11 1,midg,midg; igrid,midg,midg -1.0286789E-10 3.1146644E-11 gauss-seidel spectral radius is 0.9792977 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:27:33 rms-change max change #iterations 6.5085582E-02 9.074799 at 10iterations 5.7548149E-03 1.058773 at 20iterations 1.7210337E-03 0.3650436 at 30iterations 6.4183050E-04 0.1393776 at 40iterations 2.4066449E-04 5.2867889E-02 at 50iterations finished qdiffx linear iterations at : 15:27:36 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.4066449E-04 5.2867889E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:27:36 3.608u 0.173s 0:04.06 92.8% 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 15:27:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5487 !!! WARNING: GLM 113 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.489498 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): 24.64800 85.15400 ymin,ymax (A): 11.29600 82.99800 zmin,zma (A): -36.05200 35.17100 x,y,z range (A): 60.50600 71.70200 71.22300 scale (grids/A): 1.489498 object centre (A): 54.90100 47.14700 -0.4404984 number of atom coordinates read : 5487 total number of charged atoms : 5309 net assigned charge : -6.093958 assigned positive charge : 845.9523 centred at (gu) : 91.54672 92.92629 93.32778 assigned negative charge : -852.0540 centred at (gu) : 91.41821 92.86613 93.43069 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 91672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27863 mr = 63033 m= 2511 mr = 19094 m= 51 mr = 1105 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 526 time to turn everything in is 0.4700000 number of dielectric boundary points 38865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 615 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 39420 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) : 0.4964994 object centre at (A) : 54.90100 47.14700 -0.4404984 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0787655E-03 2.3753524E-03 midg,1,midg; midg,igrid,midg -3.3060175E-03 -1.7161567E-02 1,midg,midg; igrid,midg,midg -5.4546967E-03 4.9808822E-03 gauss-seidel spectral radius is 0.9980328 estimated iterations to convergence 179 setup time was (sec) 0.6900000 now iterating at: 15:27:37 rms-change max change #iterations 3.906039 137.8560 at 10iterations 1.576077 51.38858 at 20iterations 0.6364453 19.50033 at 30iterations 0.2563496 7.570983 at 40iterations 0.1035080 3.400547 at 50iterations 4.2025179E-02 1.389343 at 60iterations 1.7181575E-02 0.5383606 at 70iterations 7.1616410E-03 0.2362747 at 80iterations 3.1362877E-03 0.1303902 at 90iterations 1.5185408E-03 6.0087204E-02 at 100iterations 8.3519559E-04 3.9886475E-02 at 110iterations 5.1355205E-04 2.1522522E-02 at 120iterations finished qdiffx linear iterations at : 15:27:45 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 5.1355205E-04 2.1522522E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 15:27:45 8.032u 0.209s 0:08.52 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 Sun Oct 9 2011 at 15:27:45 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5487 !!! WARNING: GLM 113 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.234247 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): 24.64800 85.15400 ymin,ymax (A): 11.29600 82.99800 zmin,zma (A): -36.05200 35.17100 x,y,z range (A): 60.50600 71.70200 71.22300 scale (grids/A): 2.234247 object centre (A): 54.90100 47.14700 -0.4404984 number of atom coordinates read : 5487 total number of charged atoms : 5309 net assigned charge : -6.093958 assigned positive charge : 845.9523 centred at (gu) : 92.31942 94.38919 94.99110 assigned negative charge : -852.0540 centred at (gu) : 92.12732 94.29906 95.14613 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 213520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 97161 mr = 154801 m= 26556 mr = 76481 m= 3690 mr = 19799 m= 177 mr = 2284 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1796 time to turn everything in is 1.130000 number of dielectric boundary points 87687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 42346 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) : 1.489498 object centre at (A) : 54.90100 47.14700 -0.4404984 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9717484E-02 0.1908123 midg,1,midg; midg,igrid,midg -7.0075318E-02 -0.3140645 1,midg,midg; igrid,midg,midg -8.1305943E-02 0.1617899 gauss-seidel spectral radius is 0.9991429 estimated iterations to convergence 270 setup time was (sec) 1.390000 now iterating at: 15:27:47 rms-change max change #iterations 10.79718 271.1240 at 10iterations 6.110807 168.3821 at 20iterations 3.454009 91.20436 at 30iterations 1.933952 38.81297 at 40iterations 1.080045 23.81254 at 50iterations 0.6006618 12.98152 at 60iterations 0.3338602 6.430224 at 70iterations 0.1844573 3.573654 at 80iterations 0.1024726 2.004128 at 90iterations 5.6627311E-02 1.059662 at 100iterations 3.1280365E-02 0.5674057 at 110iterations 1.7279917E-02 0.3301744 at 120iterations 9.5770312E-03 0.1796179 at 130iterations 5.2887094E-03 0.1063156 at 140iterations 2.9304768E-03 5.2761078E-02 at 150iterations 1.6354821E-03 3.0641556E-02 at 160iterations 9.2125661E-04 1.5983582E-02 at 170iterations 5.2492891E-04 1.0322571E-02 at 180iterations finished qdiffx linear iterations at : 15:27:58 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 5.2492891E-04 1.0322571E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 15:27:59 13.263u 0.207s 0:13.76 97.8% 0+0k 0+0io 0pf+0w