Sun Oct 9 15:15:27 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 Sun Oct 9 2011 at 15:15:27 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5127023 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 0.5127023 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499961 assigned positive charge : 822.4728 centred at (gu) : 89.42684 89.03402 88.44070 assigned negative charge : -827.9792 centred at (gu) : 89.45963 89.11576 88.38097 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8655 nv = 96 ne = 84 npr = 111939 no. pairs analyzed = 111939 no. exposed pairs = 6268 no. arc points = 43589 no. surface atoms = 2099 nbur = 3286 mkacc time = 0.2400000 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 = 1.680000 m= 300 mr = 4724 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.5100000 number of dielectric boundary points 4228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4246 ## 611 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2759571E-10 7.0952154E-11 midg,1,midg; midg,igrid,midg 2.3367167E-10 -2.7631031E-10 1,midg,midg; igrid,midg,midg 2.5736158E-11 -1.6641787E-10 gauss-seidel spectral radius is 0.9805750 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 15:15:28 rms-change max change #iterations 7.3341310E-02 12.69972 at 10iterations 4.4204341E-03 0.6080952 at 20iterations 3.8947232E-04 5.1929474E-02 at 30iterations 7.3812633E-05 1.0800362E-02 at 40iterations 1.7242184E-05 2.4118423E-03 at 50iterations finished qdiffx linear iterations at : 15:15:31 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.7242184E-05 2.4118423E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 15:15:31 3.338u 0.137s 0:03.78 91.5% 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 Sun Oct 9 2011 at 15:15:31 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.538107 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 1.538107 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499961 assigned positive charge : 822.4728 centred at (gu) : 88.27874 87.10013 85.32039 assigned negative charge : -827.9792 centred at (gu) : 88.37866 87.34714 85.14273 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 99082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 28540 mr = 70001 m= 2412 mr = 19539 m= 53 mr = 1070 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3449 time to turn everything in is 0.6700000 number of dielectric boundary points 39477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 525 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 39123 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) : 0.5127023 object centre at (A) : 18.21900 130.5165 0.9630003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6803077E-03 -5.1252535E-03 midg,1,midg; midg,igrid,midg 1.4406508E-02 -1.6865697E-02 1,midg,midg; igrid,midg,midg -2.7803540E-02 -4.7374726E-03 gauss-seidel spectral radius is 0.9981692 estimated iterations to convergence 186 setup time was (sec) 0.9400000 now iterating at: 15:15:32 rms-change max change #iterations 4.150290 153.1882 at 10iterations 1.722718 58.85973 at 20iterations 0.7187256 23.39894 at 30iterations 0.2996034 9.894306 at 40iterations 0.1250243 3.657433 at 50iterations 5.1717989E-02 1.594410 at 60iterations 2.1709543E-02 0.6889629 at 70iterations 9.0498934E-03 0.2706928 at 80iterations 3.7692592E-03 0.1093814 at 90iterations 1.5801942E-03 4.4928551E-02 at 100iterations 6.6170335E-04 2.0187378E-02 at 110iterations 2.7805896E-04 8.4075928E-03 at 120iterations finished qdiffx linear iterations at : 15:15:38 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 2.7805896E-04 8.4075928E-03 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 15:15:39 7.241u 0.173s 0:07.72 95.9% 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 Sun Oct 9 2011 at 15:15:39 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5385 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.307160 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): -16.49900 52.93700 ymin,ymax (A): 97.20100 163.8320 zmin,zma (A): -29.89800 31.82400 x,y,z range (A): 69.43600 66.63100 61.72200 scale (grids/A): 2.307160 object centre (A): 18.21900 130.5165 0.9630003 number of atom coordinates read : 5385 total number of charged atoms : 5214 net assigned charge : -5.499961 assigned positive charge : 822.4728 centred at (gu) : 87.41782 85.64982 82.98033 assigned negative charge : -827.9792 centred at (gu) : 87.56797 86.02050 82.71423 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 231647 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 102996 mr = 172181 m= 26009 mr = 81609 m= 3644 mr = 19251 m= 203 mr = 2317 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 12137 time to turn everything in is 1.560000 number of dielectric boundary points 89084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 41601 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) : 1.538107 object centre at (A) : 18.21900 130.5165 0.9630003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9308459E-02 -0.1423810 midg,1,midg; midg,igrid,midg 0.2634327 -0.3775985 1,midg,midg; igrid,midg,midg -0.3645097 1.7758638E-02 gauss-seidel spectral radius is 0.9991839 estimated iterations to convergence 276 setup time was (sec) 1.850000 now iterating at: 15:15:41 rms-change max change #iterations 11.09188 318.1837 at 10iterations 6.346199 140.8973 at 20iterations 3.606626 73.34935 at 30iterations 2.043571 41.63203 at 40iterations 1.154041 25.41491 at 50iterations 0.6502166 11.56800 at 60iterations 0.3654409 8.123283 at 70iterations 0.2056681 3.470371 at 80iterations 0.1152425 2.281830 at 90iterations 6.4633705E-02 1.146954 at 100iterations 3.6149953E-02 0.6443367 at 110iterations 2.0257261E-02 0.3955975 at 120iterations 1.1335187E-02 0.1955814 at 130iterations 6.3490313E-03 0.1056061 at 140iterations 3.5531863E-03 5.7006836E-02 at 150iterations 1.9888489E-03 3.4594536E-02 at 160iterations 1.1133974E-03 1.8927097E-02 at 170iterations 6.2409200E-04 1.0974884E-02 at 180iterations finished qdiffx linear iterations at : 15:15:51 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 6.2409200E-04 1.0974884E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 15:15:51 11.826u 0.205s 0:12.31 97.6% 0+0k 0+0io 0pf+0w