Mon Oct 10 14:01:05 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 Mon Oct 10 2011 at 14:01:06 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5640140 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 0.5640140 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.864944 assigned positive charge : 778.8758 centred at (gu) : 88.39120 89.01756 89.21037 assigned negative charge : -780.7466 centred at (gu) : 88.28613 89.03685 89.17374 start vw surface at 0.2900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 10438 nv = 96 ne = 84 npr = 103034 no. pairs analyzed = 103034 no. exposed pairs = 5878 no. arc points = 39800 no. surface atoms = 2000 nbur = 3052 mkacc time = 0.2500000 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 = 1.540000 m= 488 mr = 6033 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 4875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4102 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2161265E-09 5.1806992E-10 midg,1,midg; midg,igrid,midg 3.1651809E-10 -4.8605764E-10 1,midg,midg; igrid,midg,midg -3.7990846E-09 1.4405178E-09 gauss-seidel spectral radius is 0.9839344 estimated iterations to convergence 65 setup time was (sec) 0.8600000 now iterating at: 14:01:07 rms-change max change #iterations 0.1220448 15.61872 at 10iterations 1.1287680E-02 1.647018 at 20iterations 3.0014447E-03 0.3272247 at 30iterations 1.3015779E-03 0.1510687 at 40iterations 5.8903510E-04 7.3626995E-02 at 50iterations finished qdiffx linear iterations at : 14:01:09 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 5.8903510E-04 7.3626995E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 14:01:10 3.837u 0.174s 0:04.74 84.3% 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 Mon Oct 10 2011 at 14:01:10 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.692042 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 1.692042 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.864944 assigned positive charge : 778.8758 centred at (gu) : 85.17218 87.05157 87.62959 assigned negative charge : -780.7466 centred at (gu) : 84.85837 87.11038 87.52115 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 116943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39800 grid for indexing accessible points = 1.400000 m= 40980 mr = 85196 m= 5140 mr = 29828 m= 200 mr = 2842 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.8400000 number of dielectric boundary points 45372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 37803 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) : 0.5640140 object centre at (A) : 33.75750 22.81250 30.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1728502E-02 -2.8265223E-02 midg,1,midg; midg,igrid,midg 1.8939568E-02 8.5698375E-03 1,midg,midg; igrid,midg,midg -2.5763491E-02 1.8053867E-02 gauss-seidel spectral radius is 0.9984983 estimated iterations to convergence 205 setup time was (sec) 1.150000 now iterating at: 14:01:12 rms-change max change #iterations 5.068423 168.8573 at 10iterations 2.272766 66.85683 at 20iterations 1.028834 29.22996 at 30iterations 0.4661860 11.71020 at 40iterations 0.2112768 5.966331 at 50iterations 9.5982969E-02 2.485611 at 60iterations 4.3836702E-02 1.282685 at 70iterations 2.0274360E-02 0.5614777 at 80iterations 9.7166952E-03 0.2558517 at 90iterations 4.9996893E-03 0.1318436 at 100iterations 2.8619613E-03 7.9399109E-02 at 110iterations 1.8454732E-03 5.6953430E-02 at 120iterations finished qdiffx linear iterations at : 14:01:19 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 1.8454732E-03 5.6953430E-02 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 14:01:20 8.375u 0.229s 0:09.60 89.4% 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 Mon Oct 10 2011 at 14:01:20 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.538063 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 2.538063 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.864944 assigned positive charge : 778.8758 centred at (gu) : 82.75774 85.57693 86.44395 assigned negative charge : -780.7466 centred at (gu) : 82.28764 85.66566 86.28173 start vw surface at 0.2300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 271732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39800 grid for indexing accessible points = 1.400000 m= 137385 mr = 206778 m= 44688 mr = 112491 m= 8706 mr = 35104 m= 815 mr = 6153 m= 15 mr = 450 m= 0 mr = 4 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 2.140000 number of dielectric boundary points 102361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 39212 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) : 1.692042 object centre at (A) : 33.75750 22.81250 30.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5034683 -0.6874082 midg,1,midg; midg,igrid,midg 1.2665300E-03 1.2475717E-02 1,midg,midg; igrid,midg,midg -0.4100371 0.2007475 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 2.490000 now iterating at: 14:01:23 rms-change max change #iterations 12.62963 307.3652 at 10iterations 7.490822 151.1711 at 20iterations 4.402645 104.3339 at 30iterations 2.585003 45.81111 at 40iterations 1.512191 25.74187 at 50iterations 0.8819168 15.18301 at 60iterations 0.5132802 8.611737 at 70iterations 0.2983336 4.821838 at 80iterations 0.1731455 3.009106 at 90iterations 0.1006703 1.607130 at 100iterations 5.8441687E-02 0.9399147 at 110iterations 3.4037147E-02 0.5308838 at 120iterations 1.9963004E-02 0.3056641 at 130iterations 1.1857118E-02 0.1948795 at 140iterations 7.2169993E-03 0.1219826 at 150iterations 4.5790300E-03 8.3938599E-02 at 160iterations 3.0744181E-03 5.3747177E-02 at 170iterations 2.2086045E-03 3.6850452E-02 at 180iterations finished qdiffx linear iterations at : 14:01:34 total time elapsed so far: 14.04000 # loops : 180 mean,max change (kT/e) : 2.2086045E-03 3.6850452E-02 energy calculations done at 14.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.23000 DelPhi exited at 14:01:36 14.233u 0.242s 0:15.93 90.8% 0+0k 0+0io 0pf+0w