Sat Oct 15 11:28:40 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 Sat Oct 15 2011 at 11:28:40 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 0.5438768 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 0.5438768 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499992 assigned positive charge : 504.9385 centred at (gu) : 91.15923 91.64237 90.70491 assigned negative charge : -507.4399 centred at (gu) : 91.11670 91.64120 90.67271 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6316 nv = 96 ne = 84 npr = 68729 no. pairs analyzed = 68729 no. exposed pairs = 4052 no. arc points = 28377 no. surface atoms = 1373 nbur = 1993 mkacc time = 0.1200000 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= 266 mr = 3403 m= 0 mr = 15 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2500000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2857 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1402025E-10 9.1514740E-11 midg,1,midg; midg,igrid,midg -1.0555497E-10 -2.0895771E-10 1,midg,midg; igrid,midg,midg -3.3521069E-10 1.9957271E-10 gauss-seidel spectral radius is 0.9825966 estimated iterations to convergence 62 setup time was (sec) 0.5200000 now iterating at: 11:28:41 rms-change max change #iterations 7.4653544E-02 13.78180 at 10iterations 5.0055822E-03 0.7843437 at 20iterations 3.5010005E-04 4.9743652E-02 at 30iterations 3.0908428E-05 6.4926147E-03 at 40iterations 3.9906099E-06 8.4781647E-04 at 50iterations finished qdiffx linear iterations at : 11:28:44 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 3.9906099E-06 8.4781647E-04 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 11:28:45 4.527u 0.288s 0:05.24 91.6% 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 15 2011 at 11:28:45 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 1.631630 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 1.631630 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499992 assigned positive charge : 504.9385 centred at (gu) : 93.47671 94.92641 92.11391 assigned negative charge : -507.4399 centred at (gu) : 93.34967 94.92332 92.01789 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 71132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28377 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21731 mr = 49524 m= 2274 mr = 15294 m= 64 mr = 1094 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 568 time to turn everything in is 0.3900000 number of dielectric boundary points 29287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 24643 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) : 0.5438768 object centre at (A) : 13.67850 -5.870002 8.431499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4329233E-03 2.4007440E-03 midg,1,midg; midg,igrid,midg 4.6352153E-03 -1.8925224E-03 1,midg,midg; igrid,midg,midg -5.8103092E-03 -1.4563833E-03 gauss-seidel spectral radius is 0.9982128 estimated iterations to convergence 188 setup time was (sec) 0.6900000 now iterating at: 11:28:46 rms-change max change #iterations 3.553126 182.5993 at 10iterations 1.492896 57.62671 at 20iterations 0.6265171 22.25096 at 30iterations 0.2629721 8.887196 at 40iterations 0.1106162 4.261757 at 50iterations 4.6497855E-02 1.697464 at 60iterations 1.9654024E-02 0.7123928 at 70iterations 8.2194721E-03 0.2993507 at 80iterations 3.4669221E-03 0.1149926 at 90iterations 1.4619584E-03 5.0852776E-02 at 100iterations 6.1639893E-04 2.1095276E-02 at 110iterations 2.6059602E-04 8.9902878E-03 at 120iterations finished qdiffx linear iterations at : 11:28:57 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.6059602E-04 8.9902878E-03 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 11:28:58 8.283u 0.340s 0:13.01 66.2% 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 Sat Oct 15 2011 at 11:28:58 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 2.447446 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): -15.17700 42.53400 ymin,ymax (A): -38.59800 26.85800 zmin,zma (A): -17.22800 34.09100 x,y,z range (A): 57.71100 65.45600 51.31900 scale (grids/A): 2.447446 object centre (A): 13.67850 -5.870002 8.431499 number of atom coordinates read : 3366 total number of charged atoms : 3221 net assigned charge : -2.499992 assigned positive charge : 504.9385 centred at (gu) : 95.21472 97.38945 93.17065 assigned negative charge : -507.4399 centred at (gu) : 95.02444 97.38472 93.02660 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 165601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28377 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 76601 mr = 121072 m= 21319 mr = 61484 m= 3548 mr = 16162 m= 238 mr = 2311 m= 7 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1791 time to turn everything in is 0.9300000 number of dielectric boundary points 66192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 25732 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) : 1.631630 object centre at (A) : 13.67850 -5.870002 8.431499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7624920E-02 5.8193415E-02 midg,1,midg; midg,igrid,midg 2.4123095E-02 9.4813660E-02 1,midg,midg; igrid,midg,midg -6.2548652E-02 1.4231125E-02 gauss-seidel spectral radius is 0.9991494 estimated iterations to convergence 271 setup time was (sec) 1.220000 now iterating at: 11:29:00 rms-change max change #iterations 9.125567 359.9312 at 10iterations 5.111371 125.9228 at 20iterations 2.857541 62.87679 at 30iterations 1.588332 31.99661 at 40iterations 0.8821524 18.10822 at 50iterations 0.4882151 10.19421 at 60iterations 0.2707833 5.287458 at 70iterations 0.1498021 2.977369 at 80iterations 8.2573913E-02 1.586704 at 90iterations 4.5570858E-02 1.008699 at 100iterations 2.5208838E-02 0.5745087 at 110iterations 1.3926528E-02 0.2996733 at 120iterations 7.6925787E-03 0.1506858 at 130iterations 4.2470442E-03 8.0217808E-02 at 140iterations 2.3488277E-03 4.8439026E-02 at 150iterations 1.2959805E-03 2.5192261E-02 at 160iterations 7.1593164E-04 1.8363953E-02 at 170iterations 3.9681711E-04 8.8319778E-03 at 180iterations finished qdiffx linear iterations at : 11:29:12 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 3.9681711E-04 8.8319778E-03 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 11:29:13 13.164u 0.316s 0:14.91 90.3% 0+0k 0+0io 0pf+0w