Thu Sep 17 09:28:02 PDT 2009 #!/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 Thu Sep 17 2009 at 09:28:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5932345 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 0.5932345 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3526 total number of charged atoms : 3378 net assigned charge : 2.000005 assigned positive charge : 535.3124 centred at (gu) : 88.71029 87.71910 89.96837 assigned negative charge : -533.3140 centred at (gu) : 88.71997 87.66203 89.93733 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7895 nv = 96 ne = 84 npr = 73184 no. pairs analyzed = 73184 no. exposed pairs = 3946 no. arc points = 27725 no. surface atoms = 1336 nbur = 2190 mkacc time = 0.2100000 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= 351 mr = 4469 m= 0 mr = 27 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.4400000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2875 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2265153E-10 1.9639277E-09 midg,1,midg; midg,igrid,midg -2.7392109E-09 1.7934042E-09 1,midg,midg; igrid,midg,midg 1.5079605E-09 2.6310640E-10 gauss-seidel spectral radius is 0.9853637 estimated iterations to convergence 68 setup time was (sec) 0.7700000 now iterating at: 09:28:03 rms-change max change #iterations 0.1195488 17.58251 at 10iterations 9.9217799E-03 1.456197 at 20iterations 8.4746891E-04 0.1135178 at 30iterations 7.6076612E-05 1.0108948E-02 at 40iterations 9.5580626E-06 1.5678406E-03 at 50iterations finished qdiffx linear iterations at : 09:28:08 total time elapsed so far: 5.500000 # loops : 50 mean,max change (kT/e) : 9.5580626E-06 1.5678406E-03 energy calculations done at 5.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 09:28:08 5.683u 0.364s 0:06.68 90.4% 0+0k 0+0io 4pf+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 Thu Sep 17 2009 at 09:28:08 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 = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.779703 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 1.779703 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3526 total number of charged atoms : 3378 net assigned charge : 2.000005 assigned positive charge : 535.3124 centred at (gu) : 86.13023 83.15656 89.90440 assigned negative charge : -533.3140 centred at (gu) : 86.15954 82.98563 89.81174 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27725 grid for indexing accessible points = 1.400000 m= 29668 mr = 63154 m= 3791 mr = 21831 m= 143 mr = 2240 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3678 time to turn everything in is 0.7400000 number of dielectric boundary points 34625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 26320 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) : 0.5932345 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2072788E-02 -5.8843615E-03 midg,1,midg; midg,igrid,midg -4.4867974E-03 1.2237854E-02 1,midg,midg; igrid,midg,midg 3.0432077E-02 2.9850509E-02 gauss-seidel spectral radius is 0.9985179 estimated iterations to convergence 206 setup time was (sec) 1.090000 now iterating at: 09:28:10 rms-change max change #iterations 4.406729 151.9836 at 10iterations 2.001775 64.51271 at 20iterations 0.9052473 27.56936 at 30iterations 0.4119628 12.43846 at 40iterations 0.1867113 6.092212 at 50iterations 8.5049070E-02 2.618164 at 60iterations 3.8600832E-02 1.101868 at 70iterations 1.7523061E-02 0.6055470 at 80iterations 7.9850703E-03 0.2610830 at 90iterations 3.6333674E-03 0.1079283 at 100iterations 1.6460870E-03 5.5690527E-02 at 110iterations 7.5225666E-04 2.4662018E-02 at 120iterations finished qdiffx linear iterations at : 09:28:22 total time elapsed so far: 13.05000 # loops : 120 mean,max change (kT/e) : 7.5225666E-04 2.4662018E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 09:28:23 13.208u 0.504s 0:14.28 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 Thu Sep 17 2009 at 09:28:23 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 = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.669555 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 2.669555 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3526 total number of charged atoms : 3378 net assigned charge : 2.000005 assigned positive charge : 535.3124 centred at (gu) : 84.19507 79.73450 89.85645 assigned negative charge : -533.3140 centred at (gu) : 84.23930 79.47832 89.71736 start vw surface at 0.1500000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 204556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27725 grid for indexing accessible points = 1.400000 m= 100152 mr = 152749 m= 32097 mr = 82478 m= 6352 mr = 25473 m= 635 mr = 4726 m= 11 mr = 376 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 12484 time to turn everything in is 1.900000 number of dielectric boundary points 78001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 27014 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) : 1.779703 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2935070 -6.5107942E-02 midg,1,midg; midg,igrid,midg -0.2509254 5.9829108E-02 1,midg,midg; igrid,midg,midg 0.3794946 0.3867913 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 2.310000 now iterating at: 09:28:26 rms-change max change #iterations 10.57519 305.9843 at 10iterations 6.091781 119.2889 at 20iterations 3.487440 61.06230 at 30iterations 1.996726 34.16531 at 40iterations 1.139973 22.44228 at 50iterations 0.6517392 11.47253 at 60iterations 0.3717061 6.764004 at 70iterations 0.2127149 3.851112 at 80iterations 0.1209698 2.102068 at 90iterations 6.8990968E-02 1.277328 at 100iterations 3.9292015E-02 0.6777802 at 110iterations 2.2426592E-02 0.3991272 at 120iterations 1.2802261E-02 0.2347651 at 130iterations 7.2988705E-03 0.1275826 at 140iterations 4.1695135E-03 7.6549768E-02 at 150iterations 2.3797145E-03 3.9966583E-02 at 160iterations 1.3628245E-03 2.2955894E-02 at 170iterations 7.8507373E-04 1.3389587E-02 at 180iterations finished qdiffx linear iterations at : 09:28:44 total time elapsed so far: 21.09000 # loops : 180 mean,max change (kT/e) : 7.8507373E-04 1.3389587E-02 energy calculations done at 21.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.25000 DelPhi exited at 09:28:45 21.257u 0.526s 0:22.34 97.4% 0+0k 0+0io 0pf+0w