Mon Oct 10 17:07:17 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 17:07:17 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5128427 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 0.5128427 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4143 net assigned charge : 3.400056 assigned positive charge : 653.4540 centred at (gu) : 90.61080 88.99935 87.52159 assigned negative charge : -650.0582 centred at (gu) : 90.74013 89.00008 87.63609 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7202 nv = 96 ne = 84 npr = 88271 no. pairs analyzed = 88271 no. exposed pairs = 5680 no. arc points = 39428 no. surface atoms = 1881 nbur = 2463 mkacc time = 0.1900000 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 = 1.652000 m= 268 mr = 3633 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3806 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5657929E-10 -1.3054960E-10 midg,1,midg; midg,igrid,midg 6.3383944E-11 3.5265318E-11 1,midg,midg; igrid,midg,midg 3.1864150E-10 -3.4358291E-10 gauss-seidel spectral radius is 0.9805250 estimated iterations to convergence 59 setup time was (sec) 0.6300000 now iterating at: 17:07:18 rms-change max change #iterations 6.7279994E-02 10.25527 at 10iterations 4.2022364E-03 0.6313610 at 20iterations 8.7454036E-04 0.1434517 at 30iterations 4.3931388E-04 7.2058678E-02 at 40iterations 2.2823976E-04 3.6808968E-02 at 50iterations finished qdiffx linear iterations at : 17:07:20 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.2823976E-04 3.6808968E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 17:07:21 3.332u 0.146s 0:04.25 81.6% 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 Mon Oct 10 2011 at 17:07:21 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.538528 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 1.538528 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4143 net assigned charge : 3.400056 assigned positive charge : 653.4540 centred at (gu) : 91.83099 86.99661 82.56355 assigned negative charge : -650.0582 centred at (gu) : 92.22019 87.00020 82.90794 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22897 mr = 54133 m= 2001 mr = 14861 m= 36 mr = 836 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.5700000 number of dielectric boundary points 35711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 31217 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) : 0.5128427 object centre at (A) : 14.32000 56.35600 31.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5462678E-03 -1.1345801E-02 midg,1,midg; midg,igrid,midg -2.9024535E-03 -7.3326644E-03 1,midg,midg; igrid,midg,midg 8.7010013E-03 -3.3066839E-03 gauss-seidel spectral radius is 0.9980900 estimated iterations to convergence 182 setup time was (sec) 0.8700000 now iterating at: 17:07:23 rms-change max change #iterations 3.628071 149.7943 at 10iterations 1.473797 48.92381 at 20iterations 0.5998038 21.56124 at 30iterations 0.2458401 8.249329 at 40iterations 9.9909715E-02 3.523365 at 50iterations 4.0816616E-02 1.435181 at 60iterations 1.6744595E-02 0.5535660 at 70iterations 6.9365711E-03 0.2655334 at 80iterations 2.9579673E-03 0.1065292 at 90iterations 1.3847767E-03 4.7657013E-02 at 100iterations 7.7353243E-04 2.8959274E-02 at 110iterations 5.1749434E-04 1.7230988E-02 at 120iterations finished qdiffx linear iterations at : 17:07:29 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 5.1749434E-04 1.7230988E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 17:07:30 7.628u 0.199s 0:08.19 95.3% 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 17:07:30 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.307792 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 2.307792 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4143 net assigned charge : 3.400056 assigned positive charge : 653.4540 centred at (gu) : 92.74609 85.49458 78.84480 assigned negative charge : -650.0582 centred at (gu) : 93.33024 85.50018 79.36182 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 187836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 82578 mr = 133505 m= 20569 mr = 63483 m= 2693 mr = 14533 m= 121 mr = 1539 m= 0 mr = 24 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 1.380000 number of dielectric boundary points 80713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 33054 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) : 1.538528 object centre at (A) : 14.32000 56.35600 31.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1337741 -0.2374799 midg,1,midg; midg,igrid,midg -0.1203837 -0.2499940 1,midg,midg; igrid,midg,midg 0.1028102 -3.8526818E-02 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 1.690000 now iterating at: 17:07:32 rms-change max change #iterations 9.878700 411.8872 at 10iterations 5.643684 158.7173 at 20iterations 3.194115 87.59622 at 30iterations 1.802781 39.54761 at 40iterations 1.014145 23.17473 at 50iterations 0.5662358 12.32903 at 60iterations 0.3165391 6.905036 at 70iterations 0.1764855 4.256309 at 80iterations 9.8454878E-02 2.090228 at 90iterations 5.4848667E-02 1.554294 at 100iterations 3.0466191E-02 0.6499586 at 110iterations 1.6921800E-02 0.3235149 at 120iterations 9.4380034E-03 0.1925220 at 130iterations 5.2813594E-03 0.1144176 at 140iterations 2.9971527E-03 6.4880371E-02 at 150iterations 1.7524295E-03 3.8469315E-02 at 160iterations 1.0813060E-03 2.3954391E-02 at 170iterations 7.1764365E-04 1.5710831E-02 at 180iterations finished qdiffx linear iterations at : 17:07:42 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 7.1764365E-04 1.5710831E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 17:07:43 12.578u 0.233s 0:13.19 97.0% 0+0k 0+0io 0pf+0w