Sat Oct 15 13:57:07 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 Sat Oct 15 2011 at 13:57:07 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: 381 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5110171 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 0.5110171 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4087 net assigned charge : 1.806023 assigned positive charge : 640.8603 centred at (gu) : 90.15168 90.70599 87.34052 assigned negative charge : -639.0582 centred at (gu) : 90.05510 90.74753 87.45657 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7015 nv = 96 ne = 84 npr = 87475 no. pairs analyzed = 87475 no. exposed pairs = 5645 no. arc points = 39741 no. surface atoms = 1882 nbur = 2409 mkacc time = 0.1500000 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 = 1.680000 m= 271 mr = 3474 m= 0 mr = 7 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3863 ## 587 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8716315E-10 -1.2743898E-10 midg,1,midg; midg,igrid,midg 9.5539444E-11 -9.6213509E-11 1,midg,midg; igrid,midg,midg -2.0223266E-10 2.5154534E-10 gauss-seidel spectral radius is 0.9803833 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 13:57:08 rms-change max change #iterations 6.5325350E-02 18.29965 at 10iterations 3.6886609E-03 0.6430664 at 20iterations 3.1480918E-04 4.4948578E-02 at 30iterations 8.5845953E-05 1.0350013E-02 at 40iterations 3.0711377E-05 3.7769675E-03 at 50iterations finished qdiffx linear iterations at : 13:57:15 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 3.0711377E-05 3.7769675E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 13:57:17 4.140u 0.327s 0:09.53 46.7% 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 Sat Oct 15 2011 at 13:57:18 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: 381 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.533051 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 1.533051 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4087 net assigned charge : 1.806023 assigned positive charge : 640.8603 centred at (gu) : 90.45378 92.11650 82.02032 assigned negative charge : -639.0582 centred at (gu) : 90.16532 92.24242 82.36949 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22029 mr = 52853 m= 1911 mr = 13986 m= 39 mr = 766 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.4000000 number of dielectric boundary points 35495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 517 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 30824 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) : 0.5110171 object centre at (A) : 10.48000 0.8249998 30.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0685134E-03 -1.1206291E-02 midg,1,midg; midg,igrid,midg -1.8949098E-03 -1.1212501E-02 1,midg,midg; igrid,midg,midg -1.3396400E-04 9.2622712E-03 gauss-seidel spectral radius is 0.9980708 estimated iterations to convergence 181 setup time was (sec) 0.6600000 now iterating at: 13:57:22 rms-change max change #iterations 3.579469 140.6233 at 10iterations 1.444213 48.40808 at 20iterations 0.5881612 21.61940 at 30iterations 0.2376447 7.875711 at 40iterations 9.6465677E-02 3.290192 at 50iterations 3.9108276E-02 1.201750 at 60iterations 1.5901394E-02 0.5233536 at 70iterations 6.4744633E-03 0.2062378 at 80iterations 2.6484849E-03 9.4120026E-02 at 90iterations 1.0936556E-03 4.1140079E-02 at 100iterations 4.6208809E-04 1.6559601E-02 at 110iterations 2.0825441E-04 6.9072247E-03 at 120iterations finished qdiffx linear iterations at : 13:57:44 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 2.0825441E-04 6.9072247E-03 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 13:57:46 9.162u 0.291s 0:28.16 33.5% 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 Sat Oct 15 2011 at 13:57:48 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: 381 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.299577 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): -15.52400 36.48400 ymin,ymax (A): -30.44800 32.09800 zmin,zma (A): -3.936000 65.72900 x,y,z range (A): 52.00800 62.54600 69.66499 scale (grids/A): 2.299577 object centre (A): 10.48000 0.8249998 30.89650 number of atom coordinates read : 4291 total number of charged atoms : 4087 net assigned charge : 1.806023 assigned positive charge : 640.8603 centred at (gu) : 90.68031 93.17458 78.03024 assigned negative charge : -639.0582 centred at (gu) : 90.24783 93.36354 78.55424 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 184527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 79730 mr = 130396 m= 19499 mr = 60897 m= 2672 mr = 13478 m= 156 mr = 1586 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 1.040000 number of dielectric boundary points 80187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 32600 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) : 1.533051 object centre at (A) : 10.48000 0.8249998 30.89650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1349306 -0.2624715 midg,1,midg; midg,igrid,midg -0.1093141 -0.2666529 1,midg,midg; igrid,midg,midg -8.6475937E-03 0.1517648 gauss-seidel spectral radius is 0.9991398 estimated iterations to convergence 269 setup time was (sec) 1.360000 now iterating at: 13:57:55 rms-change max change #iterations 9.728536 298.3659 at 10iterations 5.553827 128.4393 at 20iterations 3.135963 74.73150 at 30iterations 1.765934 43.62986 at 40iterations 0.9904754 22.24689 at 50iterations 0.5519186 13.45235 at 60iterations 0.3079679 7.187468 at 70iterations 0.1705843 3.806477 at 80iterations 9.4715707E-02 2.085346 at 90iterations 5.2549206E-02 1.095116 at 100iterations 2.9032949E-02 0.6233063 at 110iterations 1.6074182E-02 0.3344517 at 120iterations 8.8954289E-03 0.1804342 at 130iterations 4.9185981E-03 0.1068430 at 140iterations 2.7308974E-03 6.2705994E-02 at 150iterations 1.5224424E-03 2.9165268E-02 at 160iterations 8.5541658E-04 1.6968846E-02 at 170iterations 4.8810823E-04 1.0070801E-02 at 180iterations finished qdiffx linear iterations at : 13:58:33 total time elapsed so far: 15.06000 # loops : 180 mean,max change (kT/e) : 4.8810823E-04 1.0070801E-02 energy calculations done at 15.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.19000 DelPhi exited at 13:58:35 15.195u 0.331s 0:47.81 32.4% 0+0k 0+0io 0pf+0w