Wed Feb 15 08:55:25 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 08:55:25 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6003271 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 0.6003271 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.02304 88.77753 89.74783 assigned negative charge : -378.9426 centred at (gu) : 90.11539 88.70034 89.80337 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 52763 no. pairs analyzed = 52763 no. exposed pairs = 3635 no. arc points = 25470 no. surface atoms = 1201 nbur = 1434 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3226 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3300000 number of dielectric boundary points 3464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4834520E-09 2.0260909E-09 midg,1,midg; midg,igrid,midg 1.7087589E-09 5.2525042E-09 1,midg,midg; igrid,midg,midg 7.3904665E-09 7.9247725E-10 gauss-seidel spectral radius is 0.9856486 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 08:55:26 rms-change max change #iterations 0.1066672 16.80406 at 10iterations 8.9515476E-03 1.379908 at 20iterations 7.6620304E-04 0.1222925 at 30iterations 7.3794385E-05 1.1363983E-02 at 40iterations 1.5658830E-05 2.3365021E-03 at 50iterations finished qdiffx linear iterations at : 08:55:28 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.5658830E-05 2.3365021E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 08:55:29 3.562u 0.155s 0:04.04 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 Wed Feb 15 2012 at 08:55:29 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.800981 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 1.800981 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.06830 86.33210 89.24284 assigned negative charge : -378.9426 centred at (gu) : 90.34591 86.10072 89.40977 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25470 grid for indexing accessible points = 1.400000 m= 23739 mr = 46111 m= 3341 mr = 16609 m= 136 mr = 1841 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1598 time to turn everything in is 0.5500000 number of dielectric boundary points 31983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19333 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) : 0.6003271 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7784791E-02 -4.7517414E-03 midg,1,midg; midg,igrid,midg -6.1292772E-04 1.8799182E-02 1,midg,midg; igrid,midg,midg 2.2132684E-02 4.2880205E-03 gauss-seidel spectral radius is 0.9984929 estimated iterations to convergence 204 setup time was (sec) 0.8500000 now iterating at: 08:55:30 rms-change max change #iterations 3.778531 209.1457 at 10iterations 1.699993 64.66873 at 20iterations 0.7664425 26.86507 at 30iterations 0.3448111 11.44667 at 40iterations 0.1558184 5.515886 at 50iterations 7.0198849E-02 2.330603 at 60iterations 3.1689271E-02 1.134696 at 70iterations 1.4232501E-02 0.4806161 at 80iterations 6.4166514E-03 0.2270508 at 90iterations 2.9009758E-03 0.1044483 at 100iterations 1.3114362E-03 4.1046143E-02 at 110iterations 5.9552578E-04 1.9013405E-02 at 120iterations finished qdiffx linear iterations at : 08:55:37 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 5.9552578E-04 1.9013405E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 08:55:38 8.404u 0.210s 0:09.08 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 Wed Feb 15 2012 at 08:55:38 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2635 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.701472 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 2.701472 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2635 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.10217 84.49794 88.86391 assigned negative charge : -378.9426 centred at (gu) : 90.51878 84.15103 89.11473 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160386 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25470 grid for indexing accessible points = 1.400000 m= 77626 mr = 112693 m= 26605 mr = 61343 m= 5694 mr = 20489 m= 571 mr = 3928 m= 27 mr = 312 m= 0 mr = 2 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 5541 time to turn everything in is 1.310000 number of dielectric boundary points 72142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19960 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) : 1.800981 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4059550 -1.7456234E-02 midg,1,midg; midg,igrid,midg -0.1318264 0.1484617 1,midg,midg; igrid,midg,midg 0.2292549 5.0779935E-02 gauss-seidel spectral radius is 0.9992285 estimated iterations to convergence 284 setup time was (sec) 1.610000 now iterating at: 08:55:40 rms-change max change #iterations 9.160886 326.1421 at 10iterations 5.332146 146.4745 at 20iterations 3.084614 67.97678 at 30iterations 1.776273 43.03547 at 40iterations 1.019548 21.72608 at 50iterations 0.5849095 11.40114 at 60iterations 0.3338625 6.938249 at 70iterations 0.1903199 3.735337 at 80iterations 0.1086283 2.088222 at 90iterations 6.1898444E-02 1.193736 at 100iterations 3.5303161E-02 0.7199306 at 110iterations 2.0052833E-02 0.3969679 at 120iterations 1.1448043E-02 0.2160749 at 130iterations 6.5120864E-03 0.1448860 at 140iterations 3.6935704E-03 7.1203232E-02 at 150iterations 2.1072354E-03 4.0800095E-02 at 160iterations 1.2020729E-03 2.3643494E-02 at 170iterations 6.8874279E-04 1.3690948E-02 at 180iterations finished qdiffx linear iterations at : 08:55:51 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 6.8874279E-04 1.3690948E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 08:55:52 12.702u 0.207s 0:13.60 94.8% 0+0k 0+0io 0pf+0w