Mon Oct 10 19:32:02 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+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 Mon Oct 10 2011 at 19:32:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 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: 0.6218449 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 0.6218449 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.499968 assigned positive charge : 442.1069 centred at (gu) : 89.20513 90.48887 91.18359 assigned negative charge : -444.6082 centred at (gu) : 89.16664 90.54844 91.22932 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7726 nv = 96 ne = 84 npr = 58855 no. pairs analyzed = 58855 no. exposed pairs = 3839 no. arc points = 27335 no. surface atoms = 1290 nbur = 1655 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4095 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2200000 number of dielectric boundary points 3997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2270063E-09 -7.4100810E-09 midg,1,midg; midg,igrid,midg 2.4299387E-09 -7.6045277E-09 1,midg,midg; igrid,midg,midg -6.0966405E-09 8.6425078E-10 gauss-seidel spectral radius is 0.9866440 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 19:32:02 rms-change max change #iterations 0.1339183 19.41451 at 10iterations 1.2475823E-02 1.704073 at 20iterations 1.1835675E-03 0.1642075 at 30iterations 1.2062011E-04 1.7356873E-02 at 40iterations 1.6435002E-05 2.9230118E-03 at 50iterations finished qdiffx linear iterations at : 19:32:05 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.6435002E-05 2.9230118E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:32:06 3.435u 0.163s 0:04.21 85.2% 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 19:32:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 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: 1.865535 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 1.865535 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.499968 assigned positive charge : 442.1069 centred at (gu) : 87.61465 91.46568 93.55009 assigned negative charge : -444.6082 centred at (gu) : 87.49956 91.64507 93.68779 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 grid for indexing accessible points = 1.400000 m= 28938 mr = 56080 m= 4149 mr = 20756 m= 170 mr = 2421 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 36760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22026 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) : 0.6218449 object centre at (A) : 42.99350 27.24550 34.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3882343E-03 1.7031118E-02 midg,1,midg; midg,igrid,midg 5.1657702E-03 -2.8086910E-02 1,midg,midg; igrid,midg,midg -5.5692133E-02 1.4843039E-02 gauss-seidel spectral radius is 0.9986194 estimated iterations to convergence 213 setup time was (sec) 0.6000000 now iterating at: 19:32:07 rms-change max change #iterations 4.352060 169.3215 at 10iterations 2.019525 68.51080 at 20iterations 0.9398639 29.22309 at 30iterations 0.4364100 13.33458 at 40iterations 0.2035052 6.088703 at 50iterations 9.4966173E-02 3.498135 at 60iterations 4.4205900E-02 1.342163 at 70iterations 2.0527551E-02 0.6263461 at 80iterations 9.6051125E-03 0.3522720 at 90iterations 4.4798339E-03 0.1524429 at 100iterations 2.0900371E-03 7.3221207E-02 at 110iterations 9.7553828E-04 3.1918764E-02 at 120iterations finished qdiffx linear iterations at : 19:32:14 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 9.7553828E-04 3.1918764E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 19:32:15 7.815u 0.215s 0:08.67 92.5% 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 Mon Oct 10 2011 at 19:32:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 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: 2.798302 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): 14.36900 71.61800 ymin,ymax (A): 2.703000 51.78800 zmin,zma (A): 6.787000 62.70800 x,y,z range (A): 57.24900 49.08500 55.92100 scale (grids/A): 2.798302 object centre (A): 42.99350 27.24550 34.74750 number of atom coordinates read : 2945 total number of charged atoms : 2804 net assigned charge : -2.499968 assigned positive charge : 442.1069 centred at (gu) : 86.42186 92.19824 95.32494 assigned negative charge : -444.6082 centred at (gu) : 86.24923 92.46755 95.53159 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27335 grid for indexing accessible points = 1.400000 m= 94261 mr = 136266 m= 33140 mr = 75874 m= 7146 mr = 26036 m= 722 mr = 5142 m= 30 mr = 420 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 82993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 22426 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) : 1.865535 object centre at (A) : 42.99350 27.24550 34.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1828419 0.3036573 midg,1,midg; midg,igrid,midg 6.0534235E-02 -0.3207101 1,midg,midg; igrid,midg,midg -0.6584936 0.2784896 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.280000 now iterating at: 19:32:16 rms-change max change #iterations 10.55095 321.1478 at 10iterations 6.272398 140.9944 at 20iterations 3.698288 92.06793 at 30iterations 2.171512 41.36037 at 40iterations 1.271963 26.24989 at 50iterations 0.7404966 16.30590 at 60iterations 0.4316724 7.997311 at 70iterations 0.2508947 4.675461 at 80iterations 0.1454929 2.950668 at 90iterations 8.4255107E-02 1.572020 at 100iterations 4.8909251E-02 0.9150562 at 110iterations 2.8307170E-02 0.4953494 at 120iterations 1.6423620E-02 0.3168259 at 130iterations 9.4866147E-03 0.1705894 at 140iterations 5.4936032E-03 0.1035938 at 150iterations 3.1741057E-03 5.8467865E-02 at 160iterations 1.8357735E-03 3.4469604E-02 at 170iterations 1.0610073E-03 2.0172119E-02 at 180iterations finished qdiffx linear iterations at : 19:32:28 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.0610073E-03 2.0172119E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 19:32:29 12.920u 0.212s 0:13.75 95.4% 0+0k 0+0io 0pf+0w