Sun Oct 9 14:38:37 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 14:38:37 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7871404 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 0.7871404 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 209.3353 centred at (gu) : 89.67892 91.10543 91.66071 assigned negative charge : -209.3351 centred at (gu) : 89.63889 91.00624 91.40842 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5907 nv = 96 ne = 84 npr = 30621 no. pairs analyzed = 30621 no. exposed pairs = 1711 no. arc points = 12492 no. surface atoms = 575 nbur = 838 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3316 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1300000 number of dielectric boundary points 2965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 957 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 5941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1971368E-07 5.3558296E-07 midg,1,midg; midg,igrid,midg -1.4133772E-07 1.8624019E-07 1,midg,midg; igrid,midg,midg -7.9034670E-08 5.3303907E-08 gauss-seidel spectral radius is 0.9915050 estimated iterations to convergence 88 setup time was (sec) 0.3200000 now iterating at: 14:38:38 rms-change max change #iterations 0.2532598 40.48160 at 10iterations 3.8345307E-02 6.629118 at 20iterations 5.6723412E-03 0.8541412 at 30iterations 8.4993098E-04 0.1262054 at 40iterations 1.3011080E-04 1.8394470E-02 at 50iterations finished qdiffx linear iterations at : 14:38:41 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3011080E-04 1.8394470E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:38:41 3.335u 0.173s 0:03.78 92.5% 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 14:38:41 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.361421 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 2.361421 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 209.3353 centred at (gu) : 89.03678 93.31669 94.98241 assigned negative charge : -209.3351 centred at (gu) : 88.91680 93.01884 94.22542 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12492 grid for indexing accessible points = 1.400000 m= 24788 mr = 42421 m= 5470 mr = 18996 m= 734 mr = 3689 m= 53 mr = 428 m= 0 mr = 20 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 27026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10232 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) : 0.7871404 object centre at (A) : 25.23500 43.24650 13.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0170797E-02 8.3408296E-02 midg,1,midg; midg,igrid,midg -3.7154250E-02 1.4734975E-02 1,midg,midg; igrid,midg,midg 1.1952179E-03 -9.4913188E-03 gauss-seidel spectral radius is 0.9989603 estimated iterations to convergence 245 setup time was (sec) 0.5600000 now iterating at: 14:38:42 rms-change max change #iterations 4.510707 252.1609 at 10iterations 2.314864 94.37530 at 20iterations 1.192668 37.85315 at 30iterations 0.6179729 19.95131 at 40iterations 0.3184316 10.16906 at 50iterations 0.1644282 4.928667 at 60iterations 8.5030176E-02 2.783046 at 70iterations 4.3782815E-02 1.449944 at 80iterations 2.2575783E-02 0.7392516 at 90iterations 1.1640792E-02 0.3870678 at 100iterations 6.0249958E-03 0.1922836 at 110iterations 3.0957803E-03 9.7128868E-02 at 120iterations finished qdiffx linear iterations at : 14:38:49 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 3.0957803E-03 9.7128868E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 14:38:49 7.758u 0.189s 0:08.20 96.7% 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 Sun Oct 9 2011 at 14:38:49 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.542132 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): 8.186000 42.28400 ymin,ymax (A): 23.26900 63.22400 zmin,zma (A): -9.591001 35.63600 x,y,z range (A): 34.09800 39.95500 45.22700 scale (grids/A): 3.542132 object centre (A): 25.23500 43.24650 13.02250 number of atom coordinates read : 1413 total number of charged atoms : 1282 net assigned charge : 2.9504299E-06 assigned positive charge : 209.3353 centred at (gu) : 88.55523 94.97508 97.47358 assigned negative charge : -209.3351 centred at (gu) : 88.37521 94.52828 96.33817 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 141525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12492 grid for indexing accessible points = 1.400000 m= 75221 mr = 101765 m= 32883 mr = 62772 m= 10651 mr = 27472 m= 2815 mr = 8259 m= 541 mr = 2069 m= 76 mr = 388 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 60943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 10256 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) : 2.361421 object centre at (A) : 25.23500 43.24650 13.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5707227E-02 0.5802351 midg,1,midg; midg,igrid,midg -0.3131808 0.1516990 1,midg,midg; igrid,midg,midg 3.7099957E-02 -0.1121432 gauss-seidel spectral radius is 0.9993142 estimated iterations to convergence 301 setup time was (sec) 1.230000 now iterating at: 14:38:51 rms-change max change #iterations 9.510665 368.3618 at 10iterations 5.598179 139.3207 at 20iterations 3.281384 67.74977 at 30iterations 1.922808 34.17041 at 40iterations 1.126320 22.31520 at 50iterations 0.6603265 12.40964 at 60iterations 0.3858465 7.198553 at 70iterations 0.2259300 4.148674 at 80iterations 0.1324134 2.484508 at 90iterations 7.7601917E-02 1.332124 at 100iterations 4.5417059E-02 0.7893276 at 110iterations 2.6650665E-02 0.4784079 at 120iterations 1.5613708E-02 0.2839484 at 130iterations 9.1624968E-03 0.1551340 at 140iterations 5.3637489E-03 9.7987175E-02 at 150iterations 3.1448042E-03 6.1046600E-02 at 160iterations 1.8412689E-03 3.2538414E-02 at 170iterations 1.0819546E-03 1.9540787E-02 at 180iterations finished qdiffx linear iterations at : 14:39:02 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 1.0819546E-03 1.9540787E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 14:39:02 12.557u 0.215s 0:13.04 97.8% 0+0k 0+0io 0pf+0w