Sun Oct 9 13:51:10 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 Sun Oct 9 2011 at 13:51:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7031265 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 0.7031265 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2309 net assigned charge : 5.500019 assigned positive charge : 375.1299 centred at (gu) : 90.18710 89.70431 91.49639 assigned negative charge : -369.6305 centred at (gu) : 90.27795 89.84461 91.49783 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8288 nv = 96 ne = 84 npr = 49067 no. pairs analyzed = 49067 no. exposed pairs = 3085 no. arc points = 21900 no. surface atoms = 1033 nbur = 1418 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4608 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2080 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9203 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2104666E-08 5.4479429E-08 midg,1,midg; midg,igrid,midg 1.2205255E-07 -3.1692796E-08 1,midg,midg; igrid,midg,midg 8.6308724E-08 -7.2855748E-09 gauss-seidel spectral radius is 0.9894977 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 13:51:11 rms-change max change #iterations 0.2127351 26.22417 at 10iterations 2.6369043E-02 3.350100 at 20iterations 3.6073246E-03 0.4755592 at 30iterations 7.2050240E-04 0.1200256 at 40iterations 2.0809760E-04 3.3386230E-02 at 50iterations finished qdiffx linear iterations at : 13:51:14 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.0809760E-04 3.3386230E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 13:51:14 3.437u 0.172s 0:03.89 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 13:51:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.109380 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 2.109380 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2309 net assigned charge : 5.500019 assigned positive charge : 375.1299 centred at (gu) : 90.56059 89.11243 94.48882 assigned negative charge : -369.6305 centred at (gu) : 90.83362 89.53379 94.49316 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 33473 mr = 61080 m= 5981 mr = 24899 m= 494 mr = 3724 m= 6 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18326 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) : 0.7031265 object centre at (A) : 22.45950 61.62100 -3.1499863E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9031684E-02 3.7043173E-02 midg,1,midg; midg,igrid,midg 0.1062950 -5.5822586E-03 1,midg,midg; igrid,midg,midg 7.7483836E-03 5.6535346E-03 gauss-seidel spectral radius is 0.9988636 estimated iterations to convergence 235 setup time was (sec) 0.6600000 now iterating at: 13:51:15 rms-change max change #iterations 5.037011 281.3437 at 10iterations 2.513778 97.94928 at 20iterations 1.251999 37.30571 at 30iterations 0.6244962 16.43813 at 40iterations 0.3140563 9.297951 at 50iterations 0.1570913 4.946527 at 60iterations 7.8886658E-02 2.133485 at 70iterations 3.9524257E-02 1.115809 at 80iterations 2.0002270E-02 0.5606651 at 90iterations 1.0086729E-02 0.2989540 at 100iterations 5.1869676E-03 0.1480560 at 110iterations 2.7092702E-03 8.3187103E-02 at 120iterations finished qdiffx linear iterations at : 13:51:22 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 2.7092702E-03 8.3187103E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 13:51:23 8.040u 0.190s 0:08.51 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 13:51:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.164069 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 3.164069 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2309 net assigned charge : 5.500019 assigned positive charge : 375.1299 centred at (gu) : 90.84080 88.66843 96.73311 assigned negative charge : -369.6305 centred at (gu) : 91.25042 89.30054 96.73969 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 202351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 106107 mr = 147645 m= 40840 mr = 87174 m= 11015 mr = 32870 m= 2087 mr = 8227 m= 242 mr = 1459 m= 6 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 85116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18472 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) : 2.109380 object centre at (A) : 22.45950 61.62100 -3.1499863E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5639167 0.6063130 midg,1,midg; midg,igrid,midg 1.377289 -6.2831230E-02 1,midg,midg; igrid,midg,midg 4.5570850E-02 3.1239241E-02 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 1.560000 now iterating at: 13:51:25 rms-change max change #iterations 11.31012 488.6373 at 10iterations 6.726531 159.3303 at 20iterations 3.994771 71.96608 at 30iterations 2.367651 42.11792 at 40iterations 1.402303 25.19598 at 50iterations 0.8272078 15.73566 at 60iterations 0.4895141 7.919712 at 70iterations 0.2887430 4.998907 at 80iterations 0.1701581 3.352182 at 90iterations 0.1002682 1.671080 at 100iterations 5.9196860E-02 1.003046 at 110iterations 3.5061639E-02 0.5632691 at 120iterations 2.0955924E-02 0.3842850 at 130iterations 1.2664919E-02 0.2128143 at 140iterations 7.8465110E-03 0.1372757 at 150iterations 5.0554634E-03 9.4284058E-02 at 160iterations 3.4280198E-03 6.6993713E-02 at 170iterations 2.4742242E-03 5.4801941E-02 at 180iterations finished qdiffx linear iterations at : 13:51:36 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 2.4742242E-03 5.4801941E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 13:51:37 13.269u 0.217s 0:13.76 97.8% 0+0k 0+0io 0pf+0w