Sun Oct 9 08:34:53 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 Sun Oct 9 2011 at 08:34:53 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 = 5611 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5143691 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): -77.39400 -8.183000 ymin,ymax (A): -48.30200 12.93600 zmin,zma (A): -18.61500 50.51600 x,y,z range (A): 69.21100 61.23800 69.13100 scale (grids/A): 0.5143691 object centre (A): -42.78850 -17.68300 15.95050 number of atom coordinates read : 5611 total number of charged atoms : 5443 net assigned charge : -7.499972 assigned positive charge : 842.5715 centred at (gu) : 90.24818 89.78196 89.12597 assigned negative charge : -850.0786 centred at (gu) : 90.31267 89.71429 89.15894 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9457 nv = 96 ne = 84 npr = 112812 no. pairs analyzed = 112812 no. exposed pairs = 7036 no. arc points = 48931 no. surface atoms = 2367 nbur = 3244 mkacc time = 0.2800000 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 = 1.652000 m= 321 mr = 4924 m= 0 mr = 5 time to grow re-entrant surface = 0.3099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4774 ## 684 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 12643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7842234E-12 -1.9590149E-10 midg,1,midg; midg,igrid,midg -3.9491080E-10 1.1044899E-10 1,midg,midg; igrid,midg,midg 9.8957662E-11 -3.8554909E-10 gauss-seidel spectral radius is 0.9807315 estimated iterations to convergence 60 setup time was (sec) 0.8200000 now iterating at: 08:34:54 rms-change max change #iterations 7.5714543E-02 11.96499 at 10iterations 4.5230617E-03 0.5977402 at 20iterations 4.8086460E-04 9.9208832E-02 at 30iterations 1.3834787E-04 3.1581879E-02 at 40iterations 4.7575686E-05 1.0551453E-02 at 50iterations finished qdiffx linear iterations at : 08:34:57 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 4.7575686E-05 1.0551453E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 08:34:57 3.779u 0.172s 0:04.24 92.9% 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 08:34:57 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 = 5611 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.543107 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): -77.39400 -8.183000 ymin,ymax (A): -48.30200 12.93600 zmin,zma (A): -18.61500 50.51600 x,y,z range (A): 69.21100 61.23800 69.13100 scale (grids/A): 1.543107 object centre (A): -42.78850 -17.68300 15.95050 number of atom coordinates read : 5611 total number of charged atoms : 5443 net assigned charge : -7.499972 assigned positive charge : 842.5715 centred at (gu) : 90.74268 89.34409 87.37626 assigned negative charge : -850.0786 centred at (gu) : 90.93759 89.14292 87.47698 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 106994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31445 mr = 73922 m= 2679 mr = 20905 m= 46 mr = 1186 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1085 time to turn everything in is 0.7900000 number of dielectric boundary points 45149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 626 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 41117 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) : 0.5143691 object centre at (A) : -42.78850 -17.68300 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4450794E-03 -2.0359015E-02 midg,1,midg; midg,igrid,midg -5.7426537E-03 2.0123373E-03 1,midg,midg; igrid,midg,midg -7.1770250E-05 -2.2513615E-02 gauss-seidel spectral radius is 0.9982265 estimated iterations to convergence 189 setup time was (sec) 1.110000 now iterating at: 08:34:59 rms-change max change #iterations 4.244845 162.8196 at 10iterations 1.787202 63.43355 at 20iterations 0.7554014 24.09207 at 30iterations 0.3177759 10.32869 at 40iterations 0.1339616 3.815413 at 50iterations 5.6555122E-02 1.756256 at 60iterations 2.3915531E-02 0.7448120 at 70iterations 1.0129983E-02 0.3326607 at 80iterations 4.3131663E-03 0.1446705 at 90iterations 1.8569134E-03 5.2350998E-02 at 100iterations 8.1288727E-04 2.3871422E-02 at 110iterations 3.7302624E-04 1.3008118E-02 at 120iterations finished qdiffx linear iterations at : 08:35:06 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 3.7302624E-04 1.3008118E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 08:35:06 8.435u 0.242s 0:08.97 96.6% 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 Sun Oct 9 2011 at 08:35:06 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 = 5611 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: 2.314661 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): -77.39400 -8.183000 ymin,ymax (A): -48.30200 12.93600 zmin,zma (A): -18.61500 50.51600 x,y,z range (A): 69.21100 61.23800 69.13100 scale (grids/A): 2.314661 object centre (A): -42.78850 -17.68300 15.95050 number of atom coordinates read : 5611 total number of charged atoms : 5443 net assigned charge : -7.499972 assigned positive charge : 842.5715 centred at (gu) : 91.11340 89.01573 86.06395 assigned negative charge : -850.0786 centred at (gu) : 91.40642 88.71425 86.21532 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 249500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112390 mr = 181447 m= 28370 mr = 87665 m= 3854 mr = 20594 m= 182 mr = 2460 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 3798 time to turn everything in is 1.870000 number of dielectric boundary points 102079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 43425 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) : 1.543107 object centre at (A) : -42.78850 -17.68300 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2318340 -0.4760806 midg,1,midg; midg,igrid,midg -8.3687149E-02 6.8522818E-02 1,midg,midg; igrid,midg,midg 5.3763557E-02 -0.6303540 gauss-seidel spectral radius is 0.9992228 estimated iterations to convergence 283 setup time was (sec) 2.200000 now iterating at: 08:35:09 rms-change max change #iterations 11.54599 332.8171 at 10iterations 6.806848 172.5541 at 20iterations 3.989310 94.02145 at 30iterations 2.319240 44.81379 at 40iterations 1.341993 28.65221 at 50iterations 0.7727886 16.08418 at 60iterations 0.4447784 7.904968 at 70iterations 0.2550210 5.466601 at 80iterations 0.1464807 2.657868 at 90iterations 8.3820947E-02 1.464633 at 100iterations 4.7839336E-02 0.8107738 at 110iterations 2.7366484E-02 0.4893956 at 120iterations 1.5602525E-02 0.2710419 at 130iterations 8.9084348E-03 0.1658363 at 140iterations 5.0817574E-03 9.1705322E-02 at 150iterations 2.9096920E-03 5.2736282E-02 at 160iterations 1.6698218E-03 2.9503822E-02 at 170iterations 9.6300739E-04 1.6510010E-02 at 180iterations finished qdiffx linear iterations at : 08:35:20 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 9.6300739E-04 1.6510010E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 08:35:21 13.527u 0.175s 0:14.10 97.0% 0+0k 0+0io 0pf+0w