Mon Oct 10 17:04:21 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 17:04:21 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2984 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: HIR 148 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5526320 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): -47.01700 17.40200 ymin,ymax (A): -17.04100 28.01900 zmin,zma (A): -5.482000 42.45800 x,y,z range (A): 64.41900 45.06000 47.94000 scale (grids/A): 0.5526320 object centre (A): -14.80750 5.488999 18.48800 number of atom coordinates read : 2984 total number of charged atoms : 2843 net assigned charge : -2.985970 assigned positive charge : 449.5970 centred at (gu) : 90.24049 89.89355 89.68283 assigned negative charge : -452.5841 centred at (gu) : 90.32813 90.00863 89.58694 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5885 nv = 96 ne = 84 npr = 59813 no. pairs analyzed = 59813 no. exposed pairs = 3941 no. arc points = 27623 no. surface atoms = 1322 nbur = 1662 mkacc time = 0.1100000 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 = 1.568000 m= 236 mr = 2927 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2808 ## 365 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1631998E-09 5.3967009E-10 midg,1,midg; midg,igrid,midg 7.6691647E-10 -1.2136462E-09 1,midg,midg; igrid,midg,midg 4.8450527E-10 -1.0637716E-09 gauss-seidel spectral radius is 0.9831188 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 17:04:21 rms-change max change #iterations 7.7035435E-02 13.19997 at 10iterations 5.1896018E-03 0.7857080 at 20iterations 3.6316743E-04 5.5597305E-02 at 30iterations 2.5342822E-05 4.2533875E-03 at 40iterations 1.7940146E-06 3.1566620E-04 at 50iterations finished qdiffx linear iterations at : 17:04:24 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.7940146E-06 3.1566620E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:04:25 3.418u 0.179s 0:04.33 82.6% 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 17:04:25 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2984 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: HIR 148 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.657896 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): -47.01700 17.40200 ymin,ymax (A): -17.04100 28.01900 zmin,zma (A): -5.482000 42.45800 x,y,z range (A): 64.41900 45.06000 47.94000 scale (grids/A): 1.657896 object centre (A): -14.80750 5.488999 18.48800 number of atom coordinates read : 2984 total number of charged atoms : 2843 net assigned charge : -2.985970 assigned positive charge : 449.5970 centred at (gu) : 90.72072 89.67978 89.04736 assigned negative charge : -452.5841 centred at (gu) : 90.98412 90.02523 88.76058 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19380 mr = 43604 m= 1798 mr = 12761 m= 54 mr = 743 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 309 time to turn everything in is 0.3200000 number of dielectric boundary points 29697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 293 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21851 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) : 0.5526320 object centre at (A) : -14.80750 5.488999 18.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9599060E-02 4.7224117E-03 midg,1,midg; midg,igrid,midg 4.8085297E-03 -3.8091622E-03 1,midg,midg; igrid,midg,midg 7.8563783E-03 -2.4965843E-02 gauss-seidel spectral radius is 0.9982431 estimated iterations to convergence 189 setup time was (sec) 0.5300000 now iterating at: 17:04:26 rms-change max change #iterations 3.463572 160.7504 at 10iterations 1.457680 61.33781 at 20iterations 0.6131527 21.20277 at 30iterations 0.2590803 9.633719 at 40iterations 0.1094421 4.023212 at 50iterations 4.6235241E-02 1.770393 at 60iterations 1.9539334E-02 0.6832008 at 70iterations 8.2629062E-03 0.2755089 at 80iterations 3.4801995E-03 0.1184616 at 90iterations 1.4749888E-03 5.7490349E-02 at 100iterations 6.2237051E-04 2.0068169E-02 at 110iterations 2.6407751E-04 9.4890594E-03 at 120iterations finished qdiffx linear iterations at : 17:04:33 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.6407751E-04 9.4890594E-03 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 17:04:34 7.699u 0.200s 0:08.45 93.3% 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 17:04:34 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2984 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: HIR 148 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.486844 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): -47.01700 17.40200 ymin,ymax (A): -17.04100 28.01900 zmin,zma (A): -5.482000 42.45800 x,y,z range (A): 64.41900 45.06000 47.94000 scale (grids/A): 2.486844 object centre (A): -14.80750 5.488999 18.48800 number of atom coordinates read : 2984 total number of charged atoms : 2843 net assigned charge : -2.985970 assigned positive charge : 449.5970 centred at (gu) : 91.08081 89.51935 88.57092 assigned negative charge : -452.5841 centred at (gu) : 91.47617 90.03770 88.14072 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67625 mr = 107377 m= 18326 mr = 52254 m= 2652 mr = 13242 m= 142 mr = 1512 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1280 time to turn everything in is 0.7800000 number of dielectric boundary points 66907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22722 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) : 1.657896 object centre at (A) : -14.80750 5.488999 18.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2957882 8.5095517E-02 midg,1,midg; midg,igrid,midg 6.1095499E-02 -4.3922327E-02 1,midg,midg; igrid,midg,midg 0.4854797 -0.7605867 gauss-seidel spectral radius is 0.9991625 estimated iterations to convergence 273 setup time was (sec) 1.010000 now iterating at: 17:04:35 rms-change max change #iterations 8.946136 286.4175 at 10iterations 5.048358 125.0583 at 20iterations 2.838639 62.02682 at 30iterations 1.590228 34.40930 at 40iterations 0.8883443 21.52538 at 50iterations 0.4953311 11.61593 at 60iterations 0.2752211 6.102589 at 70iterations 0.1526337 3.699533 at 80iterations 8.4956855E-02 1.880913 at 90iterations 4.7038987E-02 0.9821587 at 100iterations 2.6077958E-02 0.5719414 at 110iterations 1.4444937E-02 0.2911358 at 120iterations 8.0089299E-03 0.1789589 at 130iterations 4.4311308E-03 9.3274117E-02 at 140iterations 2.4536331E-03 5.2001953E-02 at 150iterations 1.3553147E-03 2.8978348E-02 at 160iterations 7.5106515E-04 1.6687393E-02 at 170iterations 4.1533867E-04 8.9159012E-03 at 180iterations finished qdiffx linear iterations at : 17:04:46 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 4.1533867E-04 8.9159012E-03 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 17:04:47 12.248u 0.211s 0:12.93 96.2% 0+0k 0+0io 0pf+0w