Sun Oct 9 07:36:58 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 07:36:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 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: 0.7216997 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 0.7216997 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 252.4242 centred at (gu) : 90.10368 89.57171 89.37833 assigned negative charge : -262.5241 centred at (gu) : 90.18526 89.48843 89.68041 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5921 nv = 96 ne = 84 npr = 36851 no. pairs analyzed = 36851 no. exposed pairs = 2123 no. arc points = 14618 no. surface atoms = 718 nbur = 980 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3329 m= 1 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2300000 number of dielectric boundary points 2885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1221 ## 90 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4716612E-08 -2.6291008E-07 midg,1,midg; midg,igrid,midg -1.8090006E-07 -6.6951877E-08 1,midg,midg; igrid,midg,midg -7.1821489E-08 -1.6916472E-07 gauss-seidel spectral radius is 0.9899543 estimated iterations to convergence 81 setup time was (sec) 0.4400000 now iterating at: 07:36:58 rms-change max change #iterations 0.1986806 29.12370 at 10iterations 2.5492448E-02 3.736938 at 20iterations 3.2423893E-03 0.4613800 at 30iterations 4.1327227E-04 5.6402206E-02 at 40iterations 5.3138177E-05 8.7778270E-03 at 50iterations finished qdiffx linear iterations at : 07:37:01 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 5.3138177E-05 8.7778270E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 07:37:01 3.019u 0.156s 0:03.44 91.8% 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 07:37:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.165099 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 2.165099 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 252.4242 centred at (gu) : 90.31109 88.71529 88.13512 assigned negative charge : -262.5241 centred at (gu) : 90.55578 88.46533 89.04150 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14618 grid for indexing accessible points = 1.400000 m= 25003 mr = 43343 m= 5017 mr = 19346 m= 448 mr = 3595 m= 8 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 0.4700000 number of dielectric boundary points 26538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 12436 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) : 0.7216997 object centre at (A) : 27.43700 45.14400 14.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2584194E-02 -6.8744935E-02 midg,1,midg; midg,igrid,midg -7.0192039E-02 -9.4547952E-03 1,midg,midg; igrid,midg,midg -3.2594487E-02 -5.9473962E-02 gauss-seidel spectral radius is 0.9988339 estimated iterations to convergence 232 setup time was (sec) 0.7300000 now iterating at: 07:37:02 rms-change max change #iterations 4.388422 241.7889 at 10iterations 2.169570 100.8630 at 20iterations 1.075319 35.94352 at 30iterations 0.5320171 16.65516 at 40iterations 0.2633245 7.973091 at 50iterations 0.1309417 4.101868 at 60iterations 6.4986587E-02 2.049392 at 70iterations 3.2233793E-02 1.032875 at 80iterations 1.5961910E-02 0.4812400 at 90iterations 7.9135802E-03 0.2619841 at 100iterations 3.9155502E-03 0.1254463 at 110iterations 1.9453974E-03 6.8601608E-02 at 120iterations finished qdiffx linear iterations at : 07:37:08 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.9453974E-03 6.8601608E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 07:37:08 6.810u 0.160s 0:07.23 96.4% 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 07:37:08 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.247648 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 3.247648 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 252.4242 centred at (gu) : 90.46664 88.07281 87.20281 assigned negative charge : -262.5241 centred at (gu) : 90.83369 87.69799 88.56220 start vw surface at 0.1100000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 144001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14618 grid for indexing accessible points = 1.400000 m= 76557 mr = 103900 m= 32587 mr = 64047 m= 9717 mr = 27574 m= 1938 mr = 7958 m= 227 mr = 1541 m= 9 mr = 149 m= 0 mr = 5 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5088 time to turn everything in is 1.440000 number of dielectric boundary points 59862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 12488 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) : 2.165099 object centre at (A) : 27.43700 45.14400 14.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2797115 -0.4823425 midg,1,midg; midg,igrid,midg -0.5836570 -2.1559050E-02 1,midg,midg; igrid,midg,midg -0.1959207 -0.4155928 gauss-seidel spectral radius is 0.9992874 estimated iterations to convergence 296 setup time was (sec) 1.710000 now iterating at: 07:37:10 rms-change max change #iterations 9.659883 540.3082 at 10iterations 5.563651 138.2631 at 20iterations 3.221655 75.64286 at 30iterations 1.866766 41.49479 at 40iterations 1.084145 21.75108 at 50iterations 0.6269252 10.96091 at 60iterations 0.3633900 7.500181 at 70iterations 0.2102908 4.077148 at 80iterations 0.1219281 2.168011 at 90iterations 7.0563637E-02 1.309385 at 100iterations 4.0906843E-02 0.7066917 at 110iterations 2.3687247E-02 0.4260836 at 120iterations 1.3717665E-02 0.2483330 at 130iterations 7.9804333E-03 0.1545410 at 140iterations 4.6180100E-03 9.2689514E-02 at 150iterations 2.6746590E-03 5.3241730E-02 at 160iterations 1.5562316E-03 3.2859802E-02 at 170iterations 8.9929003E-04 1.5810013E-02 at 180iterations finished qdiffx linear iterations at : 07:37:21 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 8.9929003E-04 1.5810013E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 07:37:21 12.242u 0.191s 0:12.70 97.8% 0+0k 0+0io 0pf+0w