Wed Dec 21 14:20:44 PST 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+sph.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 = amb.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 Wed Dec 21 2011 at 14:20:44 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6108861 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 0.6108861 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 278.5881 centred at (gu) : 90.05778 89.64088 90.56942 assigned negative charge : -282.4283 centred at (gu) : 90.09911 89.60619 90.65395 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4842 nv = 96 ne = 84 npr = 39786 no. pairs analyzed = 39786 no. exposed pairs = 2398 no. arc points = 16611 no. surface atoms = 809 nbur = 1103 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 196 mr = 2684 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1649 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5826 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8416228E-10 -6.2000001E-09 midg,1,midg; midg,igrid,midg -3.8867234E-09 -9.5345609E-10 1,midg,midg; igrid,midg,midg -7.7244400E-10 -3.8877426E-09 gauss-seidel spectral radius is 0.9860677 estimated iterations to convergence 69 setup time was (sec) 0.3400000 now iterating at: 14:20:44 rms-change max change #iterations 0.1021254 17.44372 at 10iterations 8.9575071E-03 1.608075 at 20iterations 8.0137321E-04 0.1362915 at 30iterations 6.9202099E-05 1.0883331E-02 at 40iterations 6.1265077E-06 1.0299683E-03 at 50iterations finished qdiffx linear iterations at : 14:20:47 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.1265077E-06 1.0299683E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:20:48 3.317u 0.169s 0:04.21 82.4% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:20:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.832658 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 1.832658 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 278.5881 centred at (gu) : 90.17331 88.92290 91.70812 assigned negative charge : -282.4283 centred at (gu) : 90.29764 88.81910 91.96186 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 52780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16611 grid for indexing accessible points = 1.400000 m= 17660 mr = 36505 m= 2109 mr = 13135 m= 75 mr = 1222 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1446 time to turn everything in is 0.2500000 number of dielectric boundary points 21756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 13950 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) : 0.6108861 object centre at (A) : 20.01300 28.18200 17.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5133016E-04 -1.3905780E-02 midg,1,midg; midg,igrid,midg -1.9546780E-03 -2.6458281E-03 1,midg,midg; igrid,midg,midg 1.8865386E-02 1.4740176E-02 gauss-seidel spectral radius is 0.9984444 estimated iterations to convergence 201 setup time was (sec) 0.4800000 now iterating at: 14:20:49 rms-change max change #iterations 3.256118 144.1272 at 10iterations 1.444350 61.34075 at 20iterations 0.6412258 23.13837 at 30iterations 0.2867094 11.10704 at 40iterations 0.1274118 4.385933 at 50iterations 5.6458686E-02 1.962017 at 60iterations 2.5136635E-02 0.9837418 at 70iterations 1.1166217E-02 0.4268341 at 80iterations 4.9734348E-03 0.2157440 at 90iterations 2.2124390E-03 9.8564625E-02 at 100iterations 9.8773767E-04 4.0988922E-02 at 110iterations 4.3857651E-04 1.6822815E-02 at 120iterations finished qdiffx linear iterations at : 14:20:57 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 4.3857651E-04 1.6822815E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.680000 DelPhi exited at 14:20:58 8.685u 0.363s 0:09.96 90.7% 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 Wed Dec 21 2011 at 14:20:58 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.748987 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 2.748987 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 278.5881 centred at (gu) : 90.26008 88.38425 92.56223 assigned negative charge : -282.4283 centred at (gu) : 90.44651 88.22857 92.94289 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 122413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16611 grid for indexing accessible points = 1.400000 m= 59754 mr = 88829 m= 18897 mr = 49087 m= 3465 mr = 15181 m= 289 mr = 2499 m= 6 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 4954 time to turn everything in is 0.7700000 number of dielectric boundary points 49106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 14240 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) : 1.832658 object centre at (A) : 20.01300 28.18200 17.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2160003E-03 -0.1382518 midg,1,midg; midg,igrid,midg 1.4757478E-02 -2.4654459E-02 1,midg,midg; igrid,midg,midg 0.3167794 0.2674797 gauss-seidel spectral radius is 0.9991860 estimated iterations to convergence 277 setup time was (sec) 1.150000 now iterating at: 14:21:00 rms-change max change #iterations 7.810688 281.5386 at 10iterations 4.405090 117.9357 at 20iterations 2.478096 54.40478 at 30iterations 1.386508 34.36666 at 40iterations 0.7764103 18.46319 at 50iterations 0.4340711 10.78598 at 60iterations 0.2416438 5.362192 at 70iterations 0.1349767 3.425152 at 80iterations 7.5352050E-02 1.801266 at 90iterations 4.2057306E-02 0.8815408 at 100iterations 2.3448059E-02 0.5533066 at 110iterations 1.3098119E-02 0.2946568 at 120iterations 7.3109437E-03 0.1565857 at 130iterations 4.0815906E-03 8.6076736E-02 at 140iterations 2.2743682E-03 5.3771973E-02 at 150iterations 1.2684298E-03 2.9525280E-02 at 160iterations 7.0971507E-04 1.5378952E-02 at 170iterations 3.9520045E-04 8.9955330E-03 at 180iterations finished qdiffx linear iterations at : 14:21:12 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 3.9520045E-04 8.9955330E-03 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 14:21:14 14.002u 0.471s 0:15.36 94.2% 0+0k 0+0io 0pf+0w