Sun Oct 9 06:12:22 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 06:12:22 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 has a net charge of -0.0940 !!! WARNING: SEP 56 has a net charge of -0.4750 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: 0.6560640 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): 3.208000 46.92800 ymin,ymax (A): 8.681001 55.51100 zmin,zma (A): 1.065000 55.32800 x,y,z range (A): 43.72000 46.83000 54.26300 scale (grids/A): 0.6560640 object centre (A): 25.06800 32.09600 28.19650 number of atom coordinates read : 2015 total number of charged atoms : 1868 net assigned charge : 1.931017 assigned positive charge : 299.1079 centred at (gu) : 88.81190 89.15244 88.73439 assigned negative charge : -297.1771 centred at (gu) : 88.77296 89.26649 88.65202 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5824 nv = 96 ne = 84 npr = 40894 no. pairs analyzed = 40894 no. exposed pairs = 2663 no. arc points = 18674 no. surface atoms = 884 nbur = 1131 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3058 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2600000 number of dielectric boundary points 3069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1755 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0686614E-09 1.2001308E-08 midg,1,midg; midg,igrid,midg 2.3763606E-08 -9.3589554E-09 1,midg,midg; igrid,midg,midg -1.1647914E-09 7.6507432E-09 gauss-seidel spectral radius is 0.9879080 estimated iterations to convergence 74 setup time was (sec) 0.4700000 now iterating at: 06:12:22 rms-change max change #iterations 0.1419299 21.72432 at 10iterations 1.5044120E-02 2.039623 at 20iterations 1.5352742E-03 0.2302418 at 30iterations 1.5976185E-04 2.6432037E-02 at 40iterations 1.6840218E-05 2.6721954E-03 at 50iterations finished qdiffx linear iterations at : 06:12:25 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 1.6840218E-05 2.6721954E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 06:12:25 3.032u 0.144s 0:03.48 91.0% 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 06:12:25 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 has a net charge of -0.0940 !!! WARNING: SEP 56 has a net charge of -0.4750 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: 1.968192 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): 3.208000 46.92800 ymin,ymax (A): 8.681001 55.51100 zmin,zma (A): 1.065000 55.32800 x,y,z range (A): 43.72000 46.83000 54.26300 scale (grids/A): 1.968192 object centre (A): 25.06800 32.09600 28.19650 number of atom coordinates read : 2015 total number of charged atoms : 1868 net assigned charge : 1.931017 assigned positive charge : 299.1079 centred at (gu) : 86.43557 87.45724 86.20322 assigned negative charge : -297.1771 centred at (gu) : 86.31889 87.79951 85.95610 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18674 grid for indexing accessible points = 1.400000 m= 22880 mr = 41342 m= 4119 mr = 16698 m= 301 mr = 2592 m= 5 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1247 time to turn everything in is 0.4700000 number of dielectric boundary points 28150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14746 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) : 0.6560640 object centre at (A) : 25.06800 32.09600 28.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9492951E-02 -3.3953798E-03 midg,1,midg; midg,igrid,midg 1.9864734E-02 -1.2731123E-02 1,midg,midg; igrid,midg,midg 7.5539346E-03 2.3770370E-02 gauss-seidel spectral radius is 0.9986596 estimated iterations to convergence 216 setup time was (sec) 0.7300000 now iterating at: 06:12:26 rms-change max change #iterations 3.921458 238.4304 at 10iterations 1.838478 70.79691 at 20iterations 0.8654684 30.89276 at 30iterations 0.4077776 14.27856 at 40iterations 0.1918192 6.707699 at 50iterations 9.0520397E-02 3.338806 at 60iterations 4.2394564E-02 1.297821 at 70iterations 1.9957967E-02 0.6355152 at 80iterations 9.4187846E-03 0.3080444 at 90iterations 4.4309222E-03 0.1431799 at 100iterations 2.0924225E-03 7.3511124E-02 at 110iterations 9.8555069E-04 3.0595779E-02 at 120iterations finished qdiffx linear iterations at : 06:12:32 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 9.8555069E-04 3.0595779E-02 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 06:12:32 6.748u 0.168s 0:07.19 95.9% 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 06:12:33 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 has a net charge of -0.0940 !!! WARNING: SEP 56 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.952288 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): 3.208000 46.92800 ymin,ymax (A): 8.681001 55.51100 zmin,zma (A): 1.065000 55.32800 x,y,z range (A): 43.72000 46.83000 54.26300 scale (grids/A): 2.952288 object centre (A): 25.06800 32.09600 28.19650 number of atom coordinates read : 2015 total number of charged atoms : 1868 net assigned charge : 1.931017 assigned positive charge : 299.1079 centred at (gu) : 84.65331 86.18590 84.30481 assigned negative charge : -297.1771 centred at (gu) : 84.47837 86.69934 83.93412 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 142234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18674 grid for indexing accessible points = 1.400000 m= 72340 mr = 100300 m= 27929 mr = 58633 m= 7451 mr = 22395 m= 1226 mr = 5527 m= 94 mr = 856 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 4494 time to turn everything in is 1.110000 number of dielectric boundary points 63522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 14942 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) : 1.968192 object centre at (A) : 25.06800 32.09600 28.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7370738 -2.0238308E-02 midg,1,midg; midg,igrid,midg 0.2447271 -0.1069657 1,midg,midg; igrid,midg,midg 3.6015272E-02 0.2494418 gauss-seidel spectral radius is 0.9992585 estimated iterations to convergence 290 setup time was (sec) 1.390000 now iterating at: 06:12:34 rms-change max change #iterations 9.018764 442.5059 at 10iterations 5.186301 119.0078 at 20iterations 2.977801 61.61404 at 30iterations 1.715656 36.48830 at 40iterations 0.9852934 18.97622 at 50iterations 0.5654256 10.61675 at 60iterations 0.3228209 6.545172 at 70iterations 0.1858450 3.480411 at 80iterations 0.1062404 1.996958 at 90iterations 6.0945034E-02 1.199364 at 100iterations 3.4932513E-02 0.6914144 at 110iterations 1.9997837E-02 0.3807335 at 120iterations 1.1459875E-02 0.2151890 at 130iterations 6.5669273E-03 0.1242943 at 140iterations 3.7648999E-03 7.5477123E-02 at 150iterations 2.1583093E-03 4.5020103E-02 at 160iterations 1.2354229E-03 2.4761200E-02 at 170iterations 7.0678443E-04 1.3344765E-02 at 180iterations finished qdiffx linear iterations at : 06:12:43 total time elapsed so far: 10.67000 # loops : 180 mean,max change (kT/e) : 7.0678443E-04 1.3344765E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 06:12:44 10.842u 0.160s 0:11.28 97.5% 0+0k 0+0io 0pf+0w