Sat Oct 8 14:51:46 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 Sat Oct 8 2011 at 14:51:46 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 = 2988 !!! WARNING: NAP 500 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: 0.6403108 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): -12.11000 43.48800 ymin,ymax (A): -23.90800 22.76800 zmin,zma (A): -7.658000 47.64000 x,y,z range (A): 55.59800 46.67600 55.29800 scale (grids/A): 0.6403108 object centre (A): 15.68900 -0.5699997 19.99100 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 88.76462 90.04778 91.76764 assigned negative charge : -445.7114 centred at (gu) : 88.68700 89.89317 91.75939 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8142 nv = 96 ne = 84 npr = 62326 no. pairs analyzed = 62326 no. exposed pairs = 3387 no. arc points = 23630 no. surface atoms = 1165 nbur = 1823 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4751 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8447824E-10 4.4277311E-09 midg,1,midg; midg,igrid,midg -1.9006549E-08 2.2595655E-08 1,midg,midg; igrid,midg,midg -1.1311994E-08 9.4135562E-09 gauss-seidel spectral radius is 0.9873925 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 14:51:46 rms-change max change #iterations 0.1611656 21.76895 at 10iterations 1.6197635E-02 2.258804 at 20iterations 1.6784404E-03 0.2315426 at 30iterations 2.1204370E-04 2.7700424E-02 at 40iterations 3.4683431E-05 4.7760010E-03 at 50iterations finished qdiffx linear iterations at : 14:51:50 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 3.4683431E-05 4.7760010E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 14:51:50 4.270u 0.222s 0:04.80 93.5% 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 Sat Oct 8 2011 at 14:51:50 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 = 2988 !!! WARNING: NAP 500 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: 1.920932 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): -12.11000 43.48800 ymin,ymax (A): -23.90800 22.76800 zmin,zma (A): -7.658000 47.64000 x,y,z range (A): 55.59800 46.67600 55.29800 scale (grids/A): 1.920932 object centre (A): 15.68900 -0.5699997 19.99100 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 86.29323 90.14309 95.30257 assigned negative charge : -445.7114 centred at (gu) : 86.06068 89.67920 95.27804 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23630 grid for indexing accessible points = 1.400000 m= 31818 mr = 64166 m= 4758 mr = 23889 m= 290 mr = 2930 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.6300000 number of dielectric boundary points 34679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22406 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) : 0.6403108 object centre at (A) : 15.68900 -0.5699997 19.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4472835E-02 1.2317408E-02 midg,1,midg; midg,igrid,midg -2.1572287E-05 3.2610748E-02 1,midg,midg; igrid,midg,midg -4.5645818E-02 1.6145982E-02 gauss-seidel spectral radius is 0.9986882 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 14:51:52 rms-change max change #iterations 4.664556 280.9188 at 10iterations 2.225417 75.69923 at 20iterations 1.058383 32.05236 at 30iterations 0.5052170 15.37850 at 40iterations 0.2398239 7.299103 at 50iterations 0.1145797 3.261974 at 60iterations 5.4446384E-02 1.655518 at 70iterations 2.5865525E-02 0.7579203 at 80iterations 1.2355809E-02 0.3383355 at 90iterations 5.8935182E-03 0.1731148 at 100iterations 2.8060873E-03 8.5732460E-02 at 110iterations 1.3377417E-03 3.7836075E-02 at 120iterations finished qdiffx linear iterations at : 14:52:00 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.3377417E-03 3.7836075E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 14:52:01 9.720u 0.290s 0:10.37 96.5% 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 Sat Oct 8 2011 at 14:52:01 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 = 2988 !!! WARNING: NAP 500 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: 2.881398 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): -12.11000 43.48800 ymin,ymax (A): -23.90800 22.76800 zmin,zma (A): -7.658000 47.64000 x,y,z range (A): 55.59800 46.67600 55.29800 scale (grids/A): 2.881398 object centre (A): 15.68900 -0.5699997 19.99100 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 1.228008 assigned positive charge : 446.9386 centred at (gu) : 84.43967 90.21470 97.95363 assigned negative charge : -445.7114 centred at (gu) : 84.09093 89.51878 97.91695 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 206102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23630 grid for indexing accessible points = 1.400000 m= 104566 mr = 155051 m= 36753 mr = 87279 m= 8377 mr = 29607 m= 1255 mr = 6110 m= 79 mr = 827 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 289 time to turn everything in is 1.700000 number of dielectric boundary points 78234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 22744 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) : 1.920932 object centre at (A) : 15.68900 -0.5699997 19.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2514262E-02 0.2588591 midg,1,midg; midg,igrid,midg 6.9121029E-03 0.3446637 1,midg,midg; igrid,midg,midg -0.5255890 0.1427010 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 2.060000 now iterating at: 14:52:03 rms-change max change #iterations 10.86691 462.4563 at 10iterations 6.362819 137.4170 at 20iterations 3.702711 72.84734 at 30iterations 2.154072 38.86008 at 40iterations 1.248437 30.00303 at 50iterations 0.7258791 13.94464 at 60iterations 0.4201732 7.236498 at 70iterations 0.2435200 4.011487 at 80iterations 0.1410376 2.392796 at 90iterations 8.1622556E-02 1.396372 at 100iterations 4.7288340E-02 0.7732744 at 110iterations 2.7324460E-02 0.5282421 at 120iterations 1.5820459E-02 0.2824821 at 130iterations 9.1702715E-03 0.1509280 at 140iterations 5.3146230E-03 8.9284897E-02 at 150iterations 3.0768909E-03 5.2585602E-02 at 160iterations 1.7899583E-03 3.1078339E-02 at 170iterations 1.0462214E-03 1.8230438E-02 at 180iterations finished qdiffx linear iterations at : 14:52:17 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 1.0462214E-03 1.8230438E-02 energy calculations done at 15.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 14:52:18 16.077u 0.270s 0:16.66 98.0% 0+0k 0+0io 0pf+0w