Mon Oct 10 17:03:53 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 17:03:53 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: 236 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 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 : -2.999972 assigned positive charge : 447.5550 centred at (gu) : 90.23385 89.89423 89.68378 assigned negative charge : -450.5561 centred at (gu) : 90.32426 90.01065 89.58454 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 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 = 9.9999994E-02 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 = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 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 0.2700000 number of grid points assigned charge 7731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1919119E-09 5.6151628E-10 midg,1,midg; midg,igrid,midg 7.7284207E-10 -1.2220758E-09 1,midg,midg; igrid,midg,midg 5.0317056E-10 -1.0852338E-09 gauss-seidel spectral radius is 0.9831188 estimated iterations to convergence 63 setup time was (sec) 0.3900000 now iterating at: 17:03:54 rms-change max change #iterations 7.6094598E-02 12.89855 at 10iterations 5.1168026E-03 0.7968788 at 20iterations 3.5974124E-04 5.2838326E-02 at 30iterations 2.5178337E-05 4.3640137E-03 at 40iterations 1.7925306E-06 3.1661987E-04 at 50iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.7925306E-06 3.1661987E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:03:57 3.369u 0.180s 0:04.01 88.2% 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 17:03:57 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: 236 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 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: 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 : -2.999972 assigned positive charge : 447.5550 centred at (gu) : 90.70077 89.68176 89.05016 assigned negative charge : -450.5561 centred at (gu) : 90.97251 90.03131 88.75338 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 0.3900000 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 -1.9955724E-02 4.8747505E-03 midg,1,midg; midg,igrid,midg 4.8974734E-03 -3.8686309E-03 1,midg,midg; igrid,midg,midg 7.9289777E-03 -2.5145335E-02 gauss-seidel spectral radius is 0.9982431 estimated iterations to convergence 189 setup time was (sec) 0.5300000 now iterating at: 17:03:58 rms-change max change #iterations 3.444530 160.7504 at 10iterations 1.449743 61.33776 at 20iterations 0.6095559 21.36868 at 30iterations 0.2575877 9.624424 at 40iterations 0.1088056 3.920622 at 50iterations 4.5970105E-02 1.776868 at 60iterations 1.9436724E-02 0.7063103 at 70iterations 8.2164006E-03 0.2757330 at 80iterations 3.4607872E-03 0.1167450 at 90iterations 1.4665293E-03 5.7094574E-02 at 100iterations 6.1900058E-04 2.0122528E-02 at 110iterations 2.6258768E-04 9.5443726E-03 at 120iterations finished qdiffx linear iterations at : 17:04:05 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.6258768E-04 9.5443726E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 17:04:06 7.616u 0.210s 0:08.50 92.0% 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 17:04:06 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: 236 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 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 : -2.999972 assigned positive charge : 447.5550 centred at (gu) : 91.05087 89.52231 88.57515 assigned negative charge : -450.5561 centred at (gu) : 91.45872 90.04684 88.12991 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 0.7700000 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 0.8500000 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 -0.3011379 8.7356865E-02 midg,1,midg; midg,igrid,midg 6.2400386E-02 -4.4570949E-02 1,midg,midg; igrid,midg,midg 0.4865937 -0.7630805 gauss-seidel spectral radius is 0.9991625 estimated iterations to convergence 273 setup time was (sec) 1.000000 now iterating at: 17:04:07 rms-change max change #iterations 8.904413 286.4174 at 10iterations 5.025827 125.0652 at 20iterations 2.825480 62.04242 at 30iterations 1.583256 34.46159 at 40iterations 0.8844522 21.58674 at 50iterations 0.4932811 11.52231 at 60iterations 0.2740996 6.150082 at 70iterations 0.1519999 3.678809 at 80iterations 8.4621526E-02 1.887771 at 90iterations 4.6856023E-02 0.9653788 at 100iterations 2.5971936E-02 0.5623474 at 110iterations 1.4387306E-02 0.2918797 at 120iterations 7.9785604E-03 0.1801033 at 130iterations 4.4140676E-03 9.2693329E-02 at 140iterations 2.4444626E-03 5.1149368E-02 at 150iterations 1.3501302E-03 2.8827667E-02 at 160iterations 7.4830692E-04 1.6790032E-02 at 170iterations 4.1381753E-04 9.1595650E-03 at 180iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 4.1381753E-04 9.1595650E-03 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 17:04:20 12.010u 0.202s 0:13.75 88.8% 0+0k 0+0io 0pf+0w