Mon Oct 10 09:44:46 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 09:44:46 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIT 230 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5944628 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 0.5944628 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.014017 assigned positive charge : 397.6050 centred at (gu) : 88.69028 88.16738 87.42299 assigned negative charge : -391.5915 centred at (gu) : 88.75683 88.03826 87.30325 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 6574 nv = 96 ne = 84 npr = 52282 no. pairs analyzed = 52282 no. exposed pairs = 4242 no. arc points = 30920 no. surface atoms = 1403 nbur = 1312 mkacc time = 0.1200000 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= 349 mr = 2835 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7383755E-09 3.2912384E-09 midg,1,midg; midg,igrid,midg -2.7146185E-09 4.0671644E-09 1,midg,midg; igrid,midg,midg 5.7963314E-09 1.9889010E-10 gauss-seidel spectral radius is 0.9853896 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 09:44:47 rms-change max change #iterations 0.1063985 17.64018 at 10iterations 8.6779818E-03 1.529915 at 20iterations 7.2389148E-04 0.1018505 at 30iterations 6.3325278E-05 9.8800659E-03 at 40iterations 7.7320574E-06 9.9945068E-04 at 50iterations finished qdiffx linear iterations at : 09:44:49 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.7320574E-06 9.9945068E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 09:44:50 3.479u 0.211s 0:04.13 89.1% 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 09:44:50 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIT 230 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.783388 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 1.783388 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.014017 assigned positive charge : 397.6050 centred at (gu) : 86.07033 84.50140 82.26842 assigned negative charge : -391.5915 centred at (gu) : 86.27015 84.11463 81.90958 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 69609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30920 grid for indexing accessible points = 1.400000 m= 22770 mr = 41892 m= 3224 mr = 14510 m= 132 mr = 1489 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 37831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20033 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) : 0.5944628 object centre at (A) : 7.184000 -30.63450 29.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0890978E-04 4.5858910E-03 midg,1,midg; midg,igrid,midg 2.3288867E-02 3.5850037E-02 1,midg,midg; igrid,midg,midg 9.9717630E-03 3.4743184E-03 gauss-seidel spectral radius is 0.9984832 estimated iterations to convergence 204 setup time was (sec) 0.9000000 now iterating at: 09:44:51 rms-change max change #iterations 3.768763 165.7577 at 10iterations 1.683484 55.24427 at 20iterations 0.7555080 29.87201 at 30iterations 0.3372982 11.12903 at 40iterations 0.1515590 5.290562 at 50iterations 6.7864381E-02 2.666386 at 60iterations 3.0394191E-02 1.069174 at 70iterations 1.3633051E-02 0.5076599 at 80iterations 6.1113350E-03 0.2300658 at 90iterations 2.7580934E-03 0.1011186 at 100iterations 1.2342794E-03 4.2106152E-02 at 110iterations 5.5241259E-04 1.8568039E-02 at 120iterations finished qdiffx linear iterations at : 09:44:59 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 5.5241259E-04 1.8568039E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 09:44:59 8.590u 0.234s 0:09.39 93.9% 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 09:44:59 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIT 230 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.675083 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): -17.46600 31.83400 ymin,ymax (A): -60.43200 -0.8370000 zmin,zma (A): 8.9999437E-03 59.89500 x,y,z range (A): 49.30000 59.59500 59.88600 scale (grids/A): 2.675083 object centre (A): 7.184000 -30.63450 29.95200 number of atom coordinates read : 2715 total number of charged atoms : 2565 net assigned charge : 6.014017 assigned positive charge : 397.6050 centred at (gu) : 84.10534 81.75204 78.40252 assigned negative charge : -391.5915 centred at (gu) : 84.40514 81.17189 77.86422 start vw surface at 0.2100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 160693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30920 grid for indexing accessible points = 1.400000 m= 72962 mr = 103494 m= 25105 mr = 53953 m= 5231 mr = 18138 m= 510 mr = 3222 m= 14 mr = 221 m= 0 mr = 2 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 85485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20511 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) : 1.783388 object centre at (A) : 7.184000 -30.63450 29.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2999672E-02 1.6211974E-02 midg,1,midg; midg,igrid,midg 0.4816119 0.4743421 1,midg,midg; igrid,midg,midg 4.8508793E-02 2.1338303E-02 gauss-seidel spectral radius is 0.9992459 estimated iterations to convergence 287 setup time was (sec) 1.550000 now iterating at: 09:45:01 rms-change max change #iterations 9.560783 271.6771 at 10iterations 5.718419 151.4070 at 20iterations 3.370731 88.40406 at 30iterations 1.968403 45.49125 at 40iterations 1.142774 29.76080 at 50iterations 0.6640493 15.91260 at 60iterations 0.3822440 8.747271 at 70iterations 0.2201532 4.961058 at 80iterations 0.1267097 3.010664 at 90iterations 7.3003300E-02 1.690401 at 100iterations 4.1832522E-02 0.8410490 at 110iterations 2.3956977E-02 0.4840775 at 120iterations 1.3730419E-02 0.3131256 at 130iterations 7.8541404E-03 0.1773539 at 140iterations 4.4970266E-03 8.7251663E-02 at 150iterations 2.5713877E-03 5.3111076E-02 at 160iterations 1.4686327E-03 2.8458595E-02 at 170iterations 8.4170752E-04 1.7738342E-02 at 180iterations finished qdiffx linear iterations at : 09:45:11 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 8.4170752E-04 1.7738342E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 09:45:11 11.207u 0.215s 0:11.81 96.6% 0+0k 0+0io 0pf+0w