Tue Nov 8 10:15:40 PST 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 Tue Nov 8 2011 at 10:15:40 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 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: 0.5538184 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 0.5538184 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 89.72742 91.68616 90.00898 assigned negative charge : -535.8687 centred at (gu) : 89.68783 91.57581 89.96863 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7188 nv = 96 ne = 84 npr = 68937 no. pairs analyzed = 68937 no. exposed pairs = 4744 no. arc points = 33922 no. surface atoms = 1576 nbur = 1949 mkacc time = 0.1400000 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 = 1.540000 m= 300 mr = 3606 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3521 ## 494 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6147449E-10 1.9845306E-10 midg,1,midg; midg,igrid,midg -9.4272867E-10 1.4276961E-09 1,midg,midg; igrid,midg,midg -7.0000361E-10 1.7687958E-10 gauss-seidel spectral radius is 0.9832398 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 10:15:41 rms-change max change #iterations 8.5085668E-02 18.08082 at 10iterations 6.4617959E-03 0.9956436 at 20iterations 1.2676243E-03 0.2475243 at 30iterations 5.0040451E-04 0.1058273 at 40iterations 2.0843104E-04 4.4960022E-02 at 50iterations finished qdiffx linear iterations at : 10:15:44 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.0843104E-04 4.4960022E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 10:15:44 3.601u 0.185s 0:04.28 88.3% 0+0k 0+46208io 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 Tue Nov 8 2011 at 10:15:44 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.661455 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 1.661455 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 89.18143 95.05712 90.02581 assigned negative charge : -535.8687 centred at (gu) : 89.06282 94.72719 89.90554 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 79906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24361 mr = 53280 m= 2481 mr = 16287 m= 78 mr = 1111 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.4800000 number of dielectric boundary points 36146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 26041 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) : 0.5538184 object centre at (A) : 19.51250 -24.02200 3.796499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4387671E-03 -4.3197698E-03 midg,1,midg; midg,igrid,midg -1.8953499E-04 1.4904239E-02 1,midg,midg; igrid,midg,midg 5.0876532E-03 1.1775468E-02 gauss-seidel spectral radius is 0.9983273 estimated iterations to convergence 194 setup time was (sec) 0.6900000 now iterating at: 10:15:45 rms-change max change #iterations 3.863308 177.1270 at 10iterations 1.662499 56.41673 at 20iterations 0.7159594 24.32380 at 30iterations 0.3087084 10.60106 at 40iterations 0.1342275 4.358526 at 50iterations 5.7983868E-02 1.920529 at 60iterations 2.5256841E-02 0.8820038 at 70iterations 1.1177628E-02 0.3798809 at 80iterations 5.1717367E-03 0.1779499 at 90iterations 2.5854579E-03 0.1050787 at 100iterations 1.4747799E-03 6.8046570E-02 at 110iterations 9.6194830E-04 4.2137146E-02 at 120iterations finished qdiffx linear iterations at : 10:15:53 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 9.6194830E-04 4.2137146E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 10:15:53 8.060u 0.207s 0:08.77 94.1% 0+0k 0+45392io 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 Tue Nov 8 2011 at 10:15:53 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1077 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3525 !!! WARNING: TPO 164 has a net charge of -1.7500 !!! WARNING: TPO 306 has a net charge of -1.7500 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: 2.492183 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): -12.62800 51.65300 ymin,ymax (A): -54.94000 6.896000 zmin,zma (A): -22.02700 29.62000 x,y,z range (A): 64.28100 61.83600 51.64700 scale (grids/A): 2.492183 object centre (A): 19.51250 -24.02200 3.796499 number of atom coordinates read : 3525 total number of charged atoms : 3379 net assigned charge : -2.499964 assigned positive charge : 533.3667 centred at (gu) : 88.77188 97.58540 90.03866 assigned negative charge : -535.8687 centred at (gu) : 88.59402 97.09071 89.85830 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 185614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33922 grid for indexing accessible points = 1.400000 m= 84351 mr = 130632 m= 23725 mr = 65804 m= 3836 mr = 17273 m= 281 mr = 2324 m= 6 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.7800001 no. cavity mid-points inaccessible to solvent = 727 time to turn everything in is 1.210000 number of dielectric boundary points 81664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 26999 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) : 1.661455 object centre at (A) : 19.51250 -24.02200 3.796499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3995663E-02 -0.1053376 midg,1,midg; midg,igrid,midg -4.6172254E-02 0.1962388 1,midg,midg; igrid,midg,midg -8.7307533E-03 0.1017654 gauss-seidel spectral radius is 0.9992086 estimated iterations to convergence 281 setup time was (sec) 1.430000 now iterating at: 10:15:55 rms-change max change #iterations 9.929151 347.1923 at 10iterations 5.742969 173.2270 at 20iterations 3.308047 73.56609 at 30iterations 1.897573 45.84671 at 40iterations 1.085971 23.53614 at 50iterations 0.6179340 12.81319 at 60iterations 0.3520277 7.852532 at 70iterations 0.2003635 4.356818 at 80iterations 0.1135634 2.314117 at 90iterations 6.4540334E-02 1.370341 at 100iterations 3.6662109E-02 0.7126949 at 110iterations 2.0754404E-02 0.4557295 at 120iterations 1.1815217E-02 0.2504730 at 130iterations 6.7706881E-03 0.1369514 at 140iterations 3.9083189E-03 8.2405090E-02 at 150iterations 2.3158286E-03 5.3022385E-02 at 160iterations 1.4262509E-03 3.7101746E-02 at 170iterations 9.3406299E-04 2.3035049E-02 at 180iterations finished qdiffx linear iterations at : 10:16:06 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 9.3406299E-04 2.3035049E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 10:16:07 13.111u 0.246s 0:13.71 97.3% 0+0k 0+45384io 0pf+0w