Mon Oct 10 14:02:23 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 Mon Oct 10 2011 at 14:02:24 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2114 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: 0.6203821 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): -20.92800 31.02500 ymin,ymax (A): 19.41100 76.79500 zmin,zma (A): 136.0280 186.2560 x,y,z range (A): 51.95300 57.38400 50.22801 scale (grids/A): 0.6203821 object centre (A): 5.048500 48.10300 161.1420 number of atom coordinates read : 2114 total number of charged atoms : 1978 net assigned charge : -0.4999834 assigned positive charge : 305.4096 centred at (gu) : 89.81652 89.51884 90.63992 assigned negative charge : -305.9104 centred at (gu) : 89.82541 89.67142 90.52884 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5551 nv = 96 ne = 84 npr = 42628 no. pairs analyzed = 42628 no. exposed pairs = 2831 no. arc points = 20096 no. surface atoms = 956 nbur = 1158 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2834 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1915 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5879203E-09 6.1598411E-09 midg,1,midg; midg,igrid,midg 8.3208533E-09 -7.8222318E-09 1,midg,midg; igrid,midg,midg -1.3337001E-11 -9.1797792E-10 gauss-seidel spectral radius is 0.9865118 estimated iterations to convergence 70 setup time was (sec) 0.4800000 now iterating at: 14:02:24 rms-change max change #iterations 0.1112244 18.90537 at 10iterations 1.0328708E-02 1.593506 at 20iterations 9.2909409E-04 0.1335487 at 30iterations 8.4359905E-05 1.2993455E-02 at 40iterations 7.8977873E-06 1.5211105E-03 at 50iterations finished qdiffx linear iterations at : 14:02:27 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 7.8977873E-06 1.5211105E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:02:28 3.293u 0.201s 0:04.11 84.9% 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 Mon Oct 10 2011 at 14:02:28 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2114 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: 1.861146 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): -20.92800 31.02500 ymin,ymax (A): 19.41100 76.79500 zmin,zma (A): 136.0280 186.2560 x,y,z range (A): 51.95300 57.38400 50.22801 scale (grids/A): 1.861146 object centre (A): 5.048500 48.10300 161.1420 number of atom coordinates read : 2114 total number of charged atoms : 1978 net assigned charge : -0.4999834 assigned positive charge : 305.4096 centred at (gu) : 89.44946 88.55649 91.91940 assigned negative charge : -305.9104 centred at (gu) : 89.47628 89.01455 91.58672 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20096 grid for indexing accessible points = 1.400000 m= 20160 mr = 39029 m= 3267 mr = 14294 m= 186 mr = 2103 m= 1 mr = 68 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 0.4400000 number of dielectric boundary points 27536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 15522 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) : 0.6203821 object centre at (A) : 5.048500 48.10300 161.1420 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4616024E-02 1.9205933E-02 midg,1,midg; midg,igrid,midg 2.3475654E-02 -1.3908289E-02 1,midg,midg; igrid,midg,midg 2.5776777E-04 -1.4717381E-02 gauss-seidel spectral radius is 0.9985323 estimated iterations to convergence 207 setup time was (sec) 0.7200000 now iterating at: 14:02:29 rms-change max change #iterations 3.550499 180.2089 at 10iterations 1.602457 66.71058 at 20iterations 0.7311484 30.68195 at 30iterations 0.3322150 12.34154 at 40iterations 0.1506525 5.204056 at 50iterations 6.8741158E-02 2.575172 at 60iterations 3.1215277E-02 1.225334 at 70iterations 1.4151542E-02 0.5087318 at 80iterations 6.4495490E-03 0.2482972 at 90iterations 2.9384138E-03 0.1016102 at 100iterations 1.3367038E-03 5.0077319E-02 at 110iterations 6.0702401E-04 2.2490501E-02 at 120iterations finished qdiffx linear iterations at : 14:02:35 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 6.0702401E-04 2.2490501E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 14:02:36 7.389u 0.278s 0:08.21 93.1% 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 14:02:36 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2114 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: 2.791719 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): -20.92800 31.02500 ymin,ymax (A): 19.41100 76.79500 zmin,zma (A): 136.0280 186.2560 x,y,z range (A): 51.95300 57.38400 50.22801 scale (grids/A): 2.791719 object centre (A): 5.048500 48.10300 161.1420 number of atom coordinates read : 2114 total number of charged atoms : 1978 net assigned charge : -0.4999834 assigned positive charge : 305.4096 centred at (gu) : 89.17407 87.83470 92.87900 assigned negative charge : -305.9104 centred at (gu) : 89.21452 88.52185 92.38009 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 137319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20096 grid for indexing accessible points = 1.400000 m= 65100 mr = 95167 m= 23441 mr = 51776 m= 5939 mr = 18414 m= 897 mr = 4622 m= 36 mr = 650 m= 0 mr = 12 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 62091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 15824 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) : 1.861146 object centre at (A) : 5.048500 48.10300 161.1420 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2256555 0.2202676 midg,1,midg; midg,igrid,midg 0.2383569 -0.1777178 1,midg,midg; igrid,midg,midg -4.1924786E-02 -0.2169169 gauss-seidel spectral radius is 0.9992229 estimated iterations to convergence 283 setup time was (sec) 1.350000 now iterating at: 14:02:38 rms-change max change #iterations 8.475579 406.2398 at 10iterations 4.853468 116.0165 at 20iterations 2.763107 68.43581 at 30iterations 1.570546 33.52872 at 40iterations 0.8925701 20.86898 at 50iterations 0.5075245 10.51158 at 60iterations 0.2866131 5.794458 at 70iterations 0.1625066 3.181376 at 80iterations 9.2068799E-02 1.868532 at 90iterations 5.2099586E-02 1.076827 at 100iterations 2.9408732E-02 0.5883522 at 110iterations 1.6632810E-02 0.3202815 at 120iterations 9.4042607E-03 0.1966553 at 130iterations 5.3197481E-03 0.1103120 at 140iterations 3.0109750E-03 5.6812286E-02 at 150iterations 1.7023885E-03 3.6199570E-02 at 160iterations 9.6247694E-04 1.8861771E-02 at 170iterations 5.4416363E-04 1.1631012E-02 at 180iterations finished qdiffx linear iterations at : 14:02:48 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 5.4416363E-04 1.1631012E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:02:49 12.288u 0.235s 0:13.02 96.0% 0+0k 0+0io 0pf+0w