Sun Oct 9 07:00:40 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 Sun Oct 9 2011 at 07:00:40 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6927149 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): -24.38700 26.44700 ymin,ymax (A): -47.52300 -2.861000 zmin,zma (A): -23.36800 28.02400 x,y,z range (A): 50.83400 44.66200 51.39200 scale (grids/A): 0.6927149 object centre (A): 1.030000 -25.19200 2.328000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 89.01604 89.52058 89.06213 assigned negative charge : -304.1511 centred at (gu) : 88.93704 89.72820 89.00803 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6474 nv = 96 ne = 84 npr = 42728 no. pairs analyzed = 42728 no. exposed pairs = 2448 no. arc points = 17622 no. surface atoms = 825 nbur = 1176 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3579 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1700000 number of dielectric boundary points 3205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1638 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7383 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3463885E-08 8.0000190E-10 midg,1,midg; midg,igrid,midg 5.8092297E-08 -8.2016520E-08 1,midg,midg; igrid,midg,midg -5.4483813E-08 7.7083300E-09 gauss-seidel spectral radius is 0.9891370 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 07:00:40 rms-change max change #iterations 0.1919778 32.63593 at 10iterations 2.2362001E-02 3.015840 at 20iterations 2.6114490E-03 0.3863506 at 30iterations 3.0949531E-04 4.4584274E-02 at 40iterations 3.6106972E-05 5.6533813E-03 at 50iterations finished qdiffx linear iterations at : 07:00:43 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.6106972E-05 5.6533813E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 07:00:44 3.587u 0.200s 0:04.09 92.4% 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 Sun Oct 9 2011 at 07:00:44 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.078145 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): -24.38700 26.44700 ymin,ymax (A): -47.52300 -2.861000 zmin,zma (A): -23.36800 28.02400 x,y,z range (A): 50.83400 44.66200 51.39200 scale (grids/A): 2.078145 object centre (A): 1.030000 -25.19200 2.328000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 87.04798 88.56158 87.18627 assigned negative charge : -304.1511 centred at (gu) : 86.81126 89.18447 87.02414 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 25555 mr = 48053 m= 4579 mr = 19191 m= 383 mr = 3068 m= 8 mr = 189 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1511 time to turn everything in is 0.3500000 number of dielectric boundary points 29300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 14763 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) : 0.6927149 object centre at (A) : 1.030000 -25.19200 2.328000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9355631E-02 1.7377064E-02 midg,1,midg; midg,igrid,midg 6.5365501E-02 -4.4518661E-02 1,midg,midg; igrid,midg,midg -6.4590387E-02 -8.7307105E-03 gauss-seidel spectral radius is 0.9987831 estimated iterations to convergence 227 setup time was (sec) 0.5800000 now iterating at: 07:00:45 rms-change max change #iterations 4.500459 201.7836 at 10iterations 2.185635 71.84647 at 20iterations 1.064951 37.51031 at 30iterations 0.5228470 16.30281 at 40iterations 0.2539768 7.882086 at 50iterations 0.1239866 3.998653 at 60iterations 6.0662802E-02 1.908960 at 70iterations 2.9653262E-02 0.8927336 at 80iterations 1.4454730E-02 0.4695969 at 90iterations 7.0648249E-03 0.2622261 at 100iterations 3.4445322E-03 0.1058064 at 110iterations 1.6808956E-03 5.4727554E-02 at 120iterations finished qdiffx linear iterations at : 07:00:52 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.6808956E-03 5.4727554E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 07:00:52 8.072u 0.219s 0:08.57 96.6% 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 Sun Oct 9 2011 at 07:00:52 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 3.117217 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): -24.38700 26.44700 ymin,ymax (A): -47.52300 -2.861000 zmin,zma (A): -23.36800 28.02400 x,y,z range (A): 50.83400 44.66200 51.39200 scale (grids/A): 3.117217 object centre (A): 1.030000 -25.19200 2.328000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 85.57189 87.84236 85.77943 assigned negative charge : -304.1511 centred at (gu) : 85.21694 88.77660 85.53616 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 159864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17622 grid for indexing accessible points = 1.400000 m= 81527 mr = 115906 m= 30992 mr = 67430 m= 8605 mr = 25384 m= 1564 mr = 6666 m= 146 mr = 1164 m= 6 mr = 78 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 5247 time to turn everything in is 1.070000 number of dielectric boundary points 66074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14876 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) : 2.078145 object centre at (A) : 1.030000 -25.19200 2.328000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5846019 0.5563617 midg,1,midg; midg,igrid,midg 0.7517110 -0.4825821 1,midg,midg; igrid,midg,midg -0.5539557 -1.3917618E-02 gauss-seidel spectral radius is 0.9992871 estimated iterations to convergence 296 setup time was (sec) 1.330000 now iterating at: 07:00:54 rms-change max change #iterations 9.978644 409.4896 at 10iterations 5.776020 121.1183 at 20iterations 3.345154 63.86721 at 30iterations 1.940875 41.85178 at 40iterations 1.125223 23.43752 at 50iterations 0.6523710 11.40353 at 60iterations 0.3771554 7.138588 at 70iterations 0.2186212 4.002307 at 80iterations 0.1268511 2.480339 at 90iterations 7.3413447E-02 1.325347 at 100iterations 4.2491075E-02 0.7818747 at 110iterations 2.4649303E-02 0.4425392 at 120iterations 1.4254066E-02 0.2675934 at 130iterations 8.2672071E-03 0.1446533 at 140iterations 4.7929273E-03 8.5947037E-02 at 150iterations 2.7716705E-03 5.2754402E-02 at 160iterations 1.6079475E-03 2.7491570E-02 at 170iterations 9.3063078E-04 1.7955780E-02 at 180iterations finished qdiffx linear iterations at : 07:01:06 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 9.3063078E-04 1.7955780E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 07:01:06 13.537u 0.245s 0:14.06 97.9% 0+0k 0+0io 0pf+0w