Tue Oct 11 08:22:31 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 Tue Oct 11 2011 at 08:22:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 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: 0.6293755 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 0.6293755 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2471 net assigned charge : 5.000014 assigned positive charge : 392.1167 centred at (gu) : 89.83553 88.93937 90.09333 assigned negative charge : -387.1173 centred at (gu) : 89.93745 88.83842 90.23916 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6943 nv = 96 ne = 84 npr = 52395 no. pairs analyzed = 52395 no. exposed pairs = 3100 no. arc points = 22075 no. surface atoms = 1053 nbur = 1560 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3903 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3000000 number of dielectric boundary points 3356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8307 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7522309E-08 -7.5419839E-09 midg,1,midg; midg,igrid,midg -4.3780886E-09 1.1217574E-08 1,midg,midg; igrid,midg,midg 1.4697988E-08 -3.3377270E-09 gauss-seidel spectral radius is 0.9869249 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 08:22:31 rms-change max change #iterations 0.1357587 18.99988 at 10iterations 1.3855717E-02 2.017384 at 20iterations 2.0596688E-03 0.3908157 at 30iterations 5.4914044E-04 0.1221542 at 40iterations 1.7647322E-04 3.9562225E-02 at 50iterations finished qdiffx linear iterations at : 08:22:35 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.7647322E-04 3.9562225E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 08:22:36 4.252u 0.208s 0:05.07 87.7% 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 Tue Oct 11 2011 at 08:22:36 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 = 2613 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: 1.888127 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 1.888127 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2471 net assigned charge : 5.000014 assigned positive charge : 392.1167 centred at (gu) : 89.50609 86.81723 90.27924 assigned negative charge : -387.1173 centred at (gu) : 89.81168 86.51484 90.71726 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22075 grid for indexing accessible points = 1.400000 m= 27175 mr = 53248 m= 4055 mr = 20306 m= 204 mr = 2504 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1605 time to turn everything in is 0.7100000 number of dielectric boundary points 31025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19393 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) : 0.6293755 object centre at (A) : 24.33400 32.08400 29.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0035933E-02 8.1389481E-03 midg,1,midg; midg,igrid,midg -5.4948339E-03 2.0648884E-02 1,midg,midg; igrid,midg,midg 1.2991345E-03 -1.8259784E-02 gauss-seidel spectral radius is 0.9986116 estimated iterations to convergence 213 setup time was (sec) 1.070000 now iterating at: 08:22:37 rms-change max change #iterations 4.198479 174.1451 at 10iterations 1.949824 74.73753 at 20iterations 0.8997876 29.25173 at 30iterations 0.4205860 13.00705 at 40iterations 0.1960280 6.711143 at 50iterations 9.1433391E-02 2.799778 at 60iterations 4.2641953E-02 1.342453 at 70iterations 1.9975519E-02 0.6256561 at 80iterations 9.5623443E-03 0.3304443 at 90iterations 4.6300651E-03 0.1626778 at 100iterations 2.3250431E-03 8.9065552E-02 at 110iterations 1.2446574E-03 4.9453735E-02 at 120iterations finished qdiffx linear iterations at : 08:22:46 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 1.2446574E-03 4.9453735E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 08:22:47 9.966u 0.280s 0:10.77 95.0% 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 Tue Oct 11 2011 at 08:22:47 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 = 2613 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: 2.832190 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): -3.948000 52.61600 ymin,ymax (A): 5.569000 58.59900 zmin,zma (A): 8.035001 50.75600 x,y,z range (A): 56.56400 53.03000 42.72100 scale (grids/A): 2.832190 object centre (A): 24.33400 32.08400 29.39550 number of atom coordinates read : 2613 total number of charged atoms : 2471 net assigned charge : 5.000014 assigned positive charge : 392.1167 centred at (gu) : 89.25896 85.22578 90.41881 assigned negative charge : -387.1173 centred at (gu) : 89.71744 84.77214 91.07584 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22075 grid for indexing accessible points = 1.400000 m= 88852 mr = 129234 m= 31381 mr = 73399 m= 7272 mr = 25394 m= 904 mr = 5407 m= 43 mr = 558 m= 0 mr = 22 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 5616 time to turn everything in is 1.450000 number of dielectric boundary points 69930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 19767 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) : 1.888127 object centre at (A) : 24.33400 32.08400 29.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3090087 0.1283445 midg,1,midg; midg,igrid,midg 0.2379722 0.2554948 1,midg,midg; igrid,midg,midg -7.9467990E-02 -0.1654384 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.810000 now iterating at: 08:22:49 rms-change max change #iterations 9.753312 340.1668 at 10iterations 5.621644 115.8896 at 20iterations 3.227731 65.87637 at 30iterations 1.850394 41.10059 at 40iterations 1.060732 22.22418 at 50iterations 0.6083382 13.49994 at 60iterations 0.3477453 6.398760 at 70iterations 0.1987703 3.601659 at 80iterations 0.1138904 2.123978 at 90iterations 6.5400280E-02 1.244122 at 100iterations 3.7361849E-02 0.6737442 at 110iterations 2.1471934E-02 0.4484940 at 120iterations 1.2404024E-02 0.2216492 at 130iterations 7.2160522E-03 0.1465454 at 140iterations 4.2737736E-03 8.6231232E-02 at 150iterations 2.5932712E-03 5.7830811E-02 at 160iterations 1.6429558E-03 3.7261963E-02 at 170iterations 1.1053168E-03 2.9762268E-02 at 180iterations finished qdiffx linear iterations at : 08:23:03 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.1053168E-03 2.9762268E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 08:23:03 15.785u 0.285s 0:16.56 96.9% 0+0k 0+0io 0pf+0w