Sat Oct 8 12:40:10 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 8 2011 at 12:40:10 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 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: 0.5885854 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): -18.50600 26.50100 ymin,ymax (A): -15.92900 32.13400 zmin,zma (A): 16.66900 77.15300 x,y,z range (A): 45.00700 48.06300 60.48400 scale (grids/A): 0.5885854 object centre (A): 3.997499 8.102499 46.91100 number of atom coordinates read : 2346 total number of charged atoms : 2212 net assigned charge : 3.000005 assigned positive charge : 319.6136 centred at (gu) : 88.84959 89.11798 89.19530 assigned negative charge : -316.6142 centred at (gu) : 88.82712 89.19149 89.47278 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5448 nv = 96 ne = 84 npr = 49726 no. pairs analyzed = 49726 no. exposed pairs = 3113 no. arc points = 21506 no. surface atoms = 1072 nbur = 1274 mkacc time = 0.1300000 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 = 1.456000 m= 292 mr = 2681 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2138 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6769 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7176825E-09 -4.2270543E-09 midg,1,midg; midg,igrid,midg 2.8661242E-09 -5.6998090E-10 1,midg,midg; igrid,midg,midg 4.5602361E-10 9.9527109E-10 gauss-seidel spectral radius is 0.9850551 estimated iterations to convergence 67 setup time was (sec) 0.6100000 now iterating at: 12:40:11 rms-change max change #iterations 8.6581975E-02 14.66039 at 10iterations 7.7269943E-03 1.244043 at 20iterations 1.6087443E-03 0.3282013 at 30iterations 6.1511033E-04 0.1290703 at 40iterations 2.4742750E-04 5.2242279E-02 at 50iterations finished qdiffx linear iterations at : 12:40:15 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 2.4742750E-04 5.2242279E-02 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 12:40:16 4.957u 0.414s 0:05.62 95.3% 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 Sat Oct 8 2011 at 12:40:16 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 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: 1.765756 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): -18.50600 26.50100 ymin,ymax (A): -15.92900 32.13400 zmin,zma (A): 16.66900 77.15300 x,y,z range (A): 45.00700 48.06300 60.48400 scale (grids/A): 1.765756 object centre (A): 3.997499 8.102499 46.91100 number of atom coordinates read : 2346 total number of charged atoms : 2212 net assigned charge : 3.000005 assigned positive charge : 319.6136 centred at (gu) : 86.54853 87.35358 87.58556 assigned negative charge : -316.6142 centred at (gu) : 86.48145 87.57449 88.41840 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 19229 mr = 38656 m= 2676 mr = 12844 m= 101 mr = 1386 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 403 time to turn everything in is 0.5100000 number of dielectric boundary points 28226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17261 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) : 0.5885854 object centre at (A) : 3.997499 8.102499 46.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2246872E-02 -1.7324179E-02 midg,1,midg; midg,igrid,midg 6.1055268E-03 -3.5591995E-05 1,midg,midg; igrid,midg,midg -7.7750959E-04 3.4836156E-03 gauss-seidel spectral radius is 0.9983982 estimated iterations to convergence 198 setup time was (sec) 0.8200000 now iterating at: 12:40:17 rms-change max change #iterations 3.236675 182.1550 at 10iterations 1.412047 56.40929 at 20iterations 0.6201819 26.45835 at 30iterations 0.2726335 9.599642 at 40iterations 0.1202516 4.400818 at 50iterations 5.3226672E-02 2.095813 at 60iterations 2.3665782E-02 0.8583595 at 70iterations 1.0731332E-02 0.4112206 at 80iterations 5.1095271E-03 0.2075577 at 90iterations 2.6851364E-03 0.1219902 at 100iterations 1.5799215E-03 7.4584961E-02 at 110iterations 1.0455680E-03 4.4078827E-02 at 120iterations finished qdiffx linear iterations at : 12:40:27 total time elapsed so far: 11.04000 # loops : 120 mean,max change (kT/e) : 1.0455680E-03 4.4078827E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 12:40:28 11.205u 0.479s 0:11.94 97.7% 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 8 2011 at 12:40:28 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 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: 2.648634 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): -18.50600 26.50100 ymin,ymax (A): -15.92900 32.13400 zmin,zma (A): 16.66900 77.15300 x,y,z range (A): 45.00700 48.06300 60.48400 scale (grids/A): 2.648634 object centre (A): 3.997499 8.102499 46.91100 number of atom coordinates read : 2346 total number of charged atoms : 2212 net assigned charge : 3.000005 assigned positive charge : 319.6136 centred at (gu) : 84.82275 86.03020 86.37831 assigned negative charge : -316.6142 centred at (gu) : 84.72211 86.36179 87.62756 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 136895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21506 grid for indexing accessible points = 1.400000 m= 62930 mr = 94605 m= 21213 mr = 48713 m= 4358 mr = 15722 m= 417 mr = 2963 m= 6 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 1560 time to turn everything in is 1.260000 number of dielectric boundary points 63592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 17692 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) : 1.765756 object centre at (A) : 3.997499 8.102499 46.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5953068 -0.1851146 midg,1,midg; midg,igrid,midg 5.5512067E-02 1.6402013E-03 1,midg,midg; igrid,midg,midg -2.8511377E-02 2.5656989E-02 gauss-seidel spectral radius is 0.9991891 estimated iterations to convergence 277 setup time was (sec) 1.600000 now iterating at: 12:40:30 rms-change max change #iterations 7.940455 325.1422 at 10iterations 4.500302 149.1767 at 20iterations 2.535171 72.63072 at 30iterations 1.427904 30.14825 at 40iterations 0.8018537 17.80052 at 50iterations 0.4500546 11.79253 at 60iterations 0.2528151 5.571236 at 70iterations 0.1413965 3.120191 at 80iterations 7.9305604E-02 1.757542 at 90iterations 4.4497713E-02 0.9838638 at 100iterations 2.4970559E-02 0.5496750 at 110iterations 1.4073974E-02 0.3039207 at 120iterations 7.9919780E-03 0.1770525 at 130iterations 4.6015582E-03 0.1095963 at 140iterations 2.7354043E-03 7.7709198E-02 at 150iterations 1.7031361E-03 4.4555664E-02 at 160iterations 1.1435748E-03 2.9403687E-02 at 170iterations 8.2912110E-04 2.1446228E-02 at 180iterations finished qdiffx linear iterations at : 12:40:47 total time elapsed so far: 18.72000 # loops : 180 mean,max change (kT/e) : 8.2912110E-04 2.1446228E-02 energy calculations done at 18.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 12:40:48 18.890u 0.505s 0:19.66 98.6% 0+0k 0+0io 0pf+0w