Mon Oct 10 09:44:25 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 Mon Oct 10 2011 at 09:44:25 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2847 !!! WARNING: HIT 230 has a net charge of 0.5140 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: 0.5806935 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): -18.96900 34.27800 ymin,ymax (A): -60.51500 -0.9080001 zmin,zma (A): -0.8740000 60.43200 x,y,z range (A): 53.24700 59.60700 61.30600 scale (grids/A): 0.5806935 object centre (A): 7.654500 -30.71150 29.77900 number of atom coordinates read : 2847 total number of charged atoms : 2696 net assigned charge : 5.014019 assigned positive charge : 416.8668 centred at (gu) : 89.15242 87.95354 87.73964 assigned negative charge : -411.8533 centred at (gu) : 89.25391 87.78817 87.70084 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6587 nv = 96 ne = 84 npr = 55032 no. pairs analyzed = 55032 no. exposed pairs = 4315 no. arc points = 31620 no. surface atoms = 1425 nbur = 1422 mkacc time = 0.1000000 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 = 1.484000 m= 338 mr = 2891 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3098 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8227 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2045402E-10 1.1860840E-09 midg,1,midg; midg,igrid,midg -3.7844168E-09 2.8181182E-09 1,midg,midg; igrid,midg,midg 3.9756345E-09 -7.4617740E-10 gauss-seidel spectral radius is 0.9847038 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 09:44:25 rms-change max change #iterations 9.2656069E-02 16.30888 at 10iterations 7.2057731E-03 1.202316 at 20iterations 5.8316923E-04 9.1707230E-02 at 30iterations 5.4660482E-05 8.8586807E-03 at 40iterations 7.7179320E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 09:44:28 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 7.7179320E-06 1.0604858E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:44:29 3.376u 0.159s 0:03.83 91.9% 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 Mon Oct 10 2011 at 09:44:29 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2847 !!! WARNING: HIT 230 has a net charge of 0.5140 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: 1.742081 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): -18.96900 34.27800 ymin,ymax (A): -60.51500 -0.9080001 zmin,zma (A): -0.8740000 60.43200 x,y,z range (A): 53.24700 59.60700 61.30600 scale (grids/A): 1.742081 object centre (A): 7.654500 -30.71150 29.77900 number of atom coordinates read : 2847 total number of charged atoms : 2696 net assigned charge : 5.014019 assigned positive charge : 416.8668 centred at (gu) : 87.45660 83.86008 83.21846 assigned negative charge : -411.8533 centred at (gu) : 87.76153 83.36420 83.10222 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31620 grid for indexing accessible points = 1.400000 m= 22750 mr = 42938 m= 3217 mr = 14608 m= 142 mr = 1467 m= 2 mr = 14 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 0.3400000 number of dielectric boundary points 37369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20954 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) : 0.5806935 object centre at (A) : 7.654500 -30.71150 29.77900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2380278E-03 5.2159023E-03 midg,1,midg; midg,igrid,midg 2.7713142E-02 3.5101965E-02 1,midg,midg; igrid,midg,midg 1.0497200E-02 -3.8397473E-03 gauss-seidel spectral radius is 0.9984182 estimated iterations to convergence 199 setup time was (sec) 0.5500000 now iterating at: 09:44:29 rms-change max change #iterations 3.677637 155.2195 at 10iterations 1.619012 59.62650 at 20iterations 0.7134986 27.84695 at 30iterations 0.3130971 10.27499 at 40iterations 0.1374872 5.016375 at 50iterations 6.0454428E-02 2.233432 at 60iterations 2.6667090E-02 0.9261589 at 70iterations 1.1732138E-02 0.4099441 at 80iterations 5.1693353E-03 0.2097855 at 90iterations 2.2880000E-03 8.2981795E-02 at 100iterations 1.0074868E-03 3.8331985E-02 at 110iterations 4.4466046E-04 1.6407967E-02 at 120iterations finished qdiffx linear iterations at : 09:44:36 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 4.4466046E-04 1.6407967E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 09:44:37 7.694u 0.209s 0:08.32 94.8% 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 Mon Oct 10 2011 at 09:44:37 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2847 !!! WARNING: HIT 230 has a net charge of 0.5140 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: 2.613121 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): -18.96900 34.27800 ymin,ymax (A): -60.51500 -0.9080001 zmin,zma (A): -0.8740000 60.43200 x,y,z range (A): 53.24700 59.60700 61.30600 scale (grids/A): 2.613121 object centre (A): 7.654500 -30.71150 29.77900 number of atom coordinates read : 2847 total number of charged atoms : 2696 net assigned charge : 5.014019 assigned positive charge : 416.8668 centred at (gu) : 86.18489 80.79002 79.82747 assigned negative charge : -411.8533 centred at (gu) : 86.64217 80.04622 79.65320 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31620 grid for indexing accessible points = 1.400000 m= 73955 mr = 106225 m= 24917 mr = 55277 m= 5217 mr = 17960 m= 572 mr = 3170 m= 12 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 84234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21555 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) : 1.742081 object centre at (A) : 7.654500 -30.71150 29.77900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1580590 0.1006897 midg,1,midg; midg,igrid,midg 0.5639558 0.4056135 1,midg,midg; igrid,midg,midg 4.3561187E-02 -4.1260075E-02 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.120000 now iterating at: 09:44:38 rms-change max change #iterations 9.470060 304.6906 at 10iterations 5.622517 161.7271 at 20iterations 3.286182 78.09041 at 30iterations 1.904758 48.11075 at 40iterations 1.100997 26.81868 at 50iterations 0.6318465 13.73528 at 60iterations 0.3614732 7.930357 at 70iterations 0.2070369 4.321507 at 80iterations 0.1176689 2.594264 at 90iterations 6.7196973E-02 1.456956 at 100iterations 3.8230602E-02 0.7908425 at 110iterations 2.1726398E-02 0.4348927 at 120iterations 1.2334833E-02 0.2472873 at 130iterations 7.0023914E-03 0.1558590 at 140iterations 3.9714510E-03 7.9666138E-02 at 150iterations 2.2543452E-03 4.8766136E-02 at 160iterations 1.2774069E-03 2.5747299E-02 at 170iterations 7.2417216E-04 1.4625549E-02 at 180iterations finished qdiffx linear iterations at : 09:44:50 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 7.2417216E-04 1.4625549E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 09:44:50 12.976u 0.232s 0:13.53 97.5% 0+0k 0+0io 0pf+0w