Wed Feb 15 08:53:24 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:53:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2088 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 0.7222853 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 0.7222853 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2088 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 88.95547 90.29200 92.09474 assigned negative charge : -320.1891 centred at (gu) : 88.93317 90.32343 92.07211 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7455 nv = 96 ne = 84 npr = 44871 no. pairs analyzed = 44871 no. exposed pairs = 2353 no. arc points = 16165 no. surface atoms = 800 nbur = 1288 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 4603 m= 6 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 265 time to turn everything in is 0.1700000 number of dielectric boundary points 3252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1246 ## 82 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1058606E-08 -6.3738504E-08 midg,1,midg; midg,igrid,midg -3.5537852E-08 -8.5881140E-08 1,midg,midg; igrid,midg,midg -9.1141999E-08 -3.6294967E-08 gauss-seidel spectral radius is 0.9900037 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 08:53:25 rms-change max change #iterations 0.2258309 29.69775 at 10iterations 2.9056853E-02 3.716329 at 20iterations 3.7226598E-03 0.4785671 at 30iterations 4.8315930E-04 5.8645487E-02 at 40iterations 6.2789317E-05 9.1514587E-03 at 50iterations finished qdiffx linear iterations at : 08:53:28 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 6.2789317E-05 9.1514587E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:53:29 3.360u 0.174s 0:04.40 80.2% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:53:29 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2088 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 2.166856 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 2.166856 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2088 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 86.86637 90.87574 96.28387 assigned negative charge : -320.1891 centred at (gu) : 86.79958 90.97025 96.21639 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16165 grid for indexing accessible points = 1.400000 m= 33413 mr = 58071 m= 7341 mr = 26900 m= 765 mr = 5499 m= 17 mr = 530 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6735 time to turn everything in is 0.3900000 number of dielectric boundary points 29804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15529 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) : 0.7222853 object centre at (A) : -7.717000 -6.909500 -13.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2045255E-03 -3.0734662E-02 midg,1,midg; midg,igrid,midg -4.2342871E-02 -2.6224602E-02 1,midg,midg; igrid,midg,midg -4.5455635E-02 -3.2076783E-02 gauss-seidel spectral radius is 0.9988645 estimated iterations to convergence 235 setup time was (sec) 0.6100000 now iterating at: 08:53:30 rms-change max change #iterations 4.879618 222.0081 at 10iterations 2.435595 82.06941 at 20iterations 1.225933 40.10896 at 30iterations 0.6144832 19.28187 at 40iterations 0.3085780 9.917558 at 50iterations 0.1543078 4.615820 at 60iterations 7.7548191E-02 2.269775 at 70iterations 3.8780853E-02 1.150336 at 80iterations 1.9494263E-02 0.5682678 at 90iterations 9.7602243E-03 0.3111136 at 100iterations 4.9037235E-03 0.1424112 at 110iterations 2.4538133E-03 6.3901901E-02 at 120iterations finished qdiffx linear iterations at : 08:53:38 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 2.4538133E-03 6.3901901E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 08:53:39 8.641u 0.217s 0:09.53 92.8% 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 Wed Feb 15 2012 at 08:53:39 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2088 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 3.250284 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 3.250284 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2088 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 85.29945 91.31367 99.42571 assigned negative charge : -320.1891 centred at (gu) : 85.19939 91.45542 99.32465 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 182859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16165 grid for indexing accessible points = 1.400000 m= 102137 mr = 139082 m= 45110 mr = 87768 m= 14342 mr = 39052 m= 3230 mr = 12060 m= 465 mr = 2625 m= 13 mr = 353 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 22772 time to turn everything in is 1.260000 number of dielectric boundary points 67216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 15616 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) : 2.166856 object centre at (A) : -7.717000 -6.909500 -13.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8291760E-02 -0.4261663 midg,1,midg; midg,igrid,midg -0.7014399 -0.2828869 1,midg,midg; igrid,midg,midg -0.3256295 -0.2982152 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 1.550000 now iterating at: 08:53:41 rms-change max change #iterations 10.66291 390.3674 at 10iterations 6.247241 118.6632 at 20iterations 3.657561 70.46329 at 30iterations 2.130872 39.42792 at 40iterations 1.246033 21.65850 at 50iterations 0.7290710 13.09524 at 60iterations 0.4249153 7.152439 at 70iterations 0.2477173 4.650451 at 80iterations 0.1444964 2.361339 at 90iterations 8.4434465E-02 1.402268 at 100iterations 4.9246572E-02 0.8327293 at 110iterations 2.8675741E-02 0.4535027 at 120iterations 1.6783774E-02 0.2690239 at 130iterations 9.7720772E-03 0.1596117 at 140iterations 5.7104826E-03 9.6382141E-02 at 150iterations 3.3348554E-03 5.4788589E-02 at 160iterations 1.9435291E-03 3.4896851E-02 at 170iterations 1.1339627E-03 1.9134521E-02 at 180iterations finished qdiffx linear iterations at : 08:53:54 total time elapsed so far: 14.83000 # loops : 180 mean,max change (kT/e) : 1.1339627E-03 1.9134521E-02 energy calculations done at 14.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.95000 DelPhi exited at 08:53:55 14.951u 0.318s 0:15.90 95.9% 0+0k 0+0io 0pf+0w