Sat Oct 8 13:57:30 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 Sat Oct 8 2011 at 13:57:30 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3027 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6524329 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 0.6524329 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 1.4008060E-02 assigned positive charge : 455.5376 centred at (gu) : 88.99520 90.03739 91.58876 assigned negative charge : -455.5243 centred at (gu) : 88.97911 89.93912 91.50626 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8532 nv = 96 ne = 84 npr = 63428 no. pairs analyzed = 63428 no. exposed pairs = 3472 no. arc points = 23963 no. surface atoms = 1180 nbur = 1847 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 4970 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3200000 number of dielectric boundary points 3977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1443657E-08 2.1654300E-08 midg,1,midg; midg,igrid,midg -1.8951052E-08 1.8440099E-08 1,midg,midg; igrid,midg,midg -4.0688386E-09 2.2987412E-09 gauss-seidel spectral radius is 0.9878570 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 13:57:30 rms-change max change #iterations 0.1772248 21.57202 at 10iterations 1.8568955E-02 2.206858 at 20iterations 2.0591298E-03 0.2678261 at 30iterations 2.6105047E-04 3.4605026E-02 at 40iterations 4.2892389E-05 5.6667328E-03 at 50iterations finished qdiffx linear iterations at : 13:57:33 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 4.2892389E-05 5.6667328E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 13:57:33 3.158u 0.138s 0:03.61 90.8% 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 Sat Oct 8 2011 at 13:57:33 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3027 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.957299 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 1.957299 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 1.4008060E-02 assigned positive charge : 455.5376 centred at (gu) : 86.98499 90.11163 94.76597 assigned negative charge : -455.5243 centred at (gu) : 86.93697 89.81716 94.51851 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 92815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23963 grid for indexing accessible points = 1.400000 m= 34351 mr = 67164 m= 5410 mr = 25887 m= 363 mr = 3403 m= 4 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 36380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22766 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) : 0.6524329 object centre at (A) : 15.09200 -0.6335001 20.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1576189E-02 2.7598342E-02 midg,1,midg; midg,igrid,midg -3.0557429E-03 2.4976151E-02 1,midg,midg; igrid,midg,midg -4.3178018E-02 1.8252790E-02 gauss-seidel spectral radius is 0.9987375 estimated iterations to convergence 223 setup time was (sec) 0.8800000 now iterating at: 13:57:34 rms-change max change #iterations 4.899950 181.9152 at 10iterations 2.375200 74.16455 at 20iterations 1.140161 34.82632 at 30iterations 0.5540627 14.62446 at 40iterations 0.2668991 7.086027 at 50iterations 0.1289833 3.766258 at 60iterations 6.2266372E-02 1.618459 at 70iterations 3.0054981E-02 0.8642731 at 80iterations 1.4563179E-02 0.3849411 at 90iterations 7.0296745E-03 0.1991844 at 100iterations 3.4025505E-03 9.1941833E-02 at 110iterations 1.6516868E-03 4.8743248E-02 at 120iterations finished qdiffx linear iterations at : 13:57:41 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 1.6516868E-03 4.8743248E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 13:57:41 7.513u 0.194s 0:08.05 95.6% 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 Sat Oct 8 2011 at 13:57:41 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3027 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.935948 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): -11.97300 42.15700 ymin,ymax (A): -23.59900 22.33200 zmin,zma (A): -7.208000 47.35700 x,y,z range (A): 54.13000 45.93100 54.56500 scale (grids/A): 2.935948 object centre (A): 15.09200 -0.6335001 20.07450 number of atom coordinates read : 3027 total number of charged atoms : 2880 net assigned charge : 1.4008060E-02 assigned positive charge : 455.5376 centred at (gu) : 85.47740 90.16740 97.14879 assigned negative charge : -455.5243 centred at (gu) : 85.40529 89.72572 96.77765 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 215087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23963 grid for indexing accessible points = 1.400000 m= 111734 mr = 162157 m= 40479 mr = 93302 m= 9810 mr = 32899 m= 1535 mr = 7248 m= 93 mr = 1022 m= 6 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 82091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 23039 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) : 1.957299 object centre at (A) : 15.09200 -0.6335001 20.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0529285E-02 0.5152892 midg,1,midg; midg,igrid,midg -2.7190106E-02 0.2796587 1,midg,midg; igrid,midg,midg -0.4492997 0.2657185 gauss-seidel spectral radius is 0.9992894 estimated iterations to convergence 296 setup time was (sec) 1.890000 now iterating at: 13:57:44 rms-change max change #iterations 11.27790 366.7790 at 10iterations 6.638144 124.1076 at 20iterations 3.892939 69.24384 at 30iterations 2.279216 43.95501 at 40iterations 1.332668 21.49126 at 50iterations 0.7778428 13.37342 at 60iterations 0.4536570 7.866298 at 70iterations 0.2641177 4.482024 at 80iterations 0.1538563 2.454922 at 90iterations 8.9628980E-02 1.323073 at 100iterations 5.2181754E-02 0.7994041 at 110iterations 3.0358724E-02 0.5193787 at 120iterations 1.7698037E-02 0.3021774 at 130iterations 1.0342468E-02 0.1639910 at 140iterations 6.0443957E-03 9.7023726E-02 at 150iterations 3.5311580E-03 5.9969425E-02 at 160iterations 2.0822170E-03 3.3665657E-02 at 170iterations 1.2375475E-03 2.0362854E-02 at 180iterations finished qdiffx linear iterations at : 13:57:53 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 1.2375475E-03 2.0362854E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 13:57:54 11.772u 0.186s 0:12.29 97.2% 0+0k 0+0io 0pf+0w