Wed Feb 15 08:54:24 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 08:54:24 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 = 2817 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: 0.6306689 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 0.6306689 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 90.29443 90.42963 89.56448 assigned negative charge : -430.4511 centred at (gu) : 90.46569 90.41255 89.85503 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7285 nv = 96 ne = 84 npr = 58338 no. pairs analyzed = 58338 no. exposed pairs = 3351 no. arc points = 23336 no. surface atoms = 1129 nbur = 1688 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 4063 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 78 time to turn everything in is 0.2100000 number of dielectric boundary points 3529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2336 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0347298E-08 -2.7787868E-08 midg,1,midg; midg,igrid,midg -2.0906237E-09 1.2338695E-09 1,midg,midg; igrid,midg,midg 1.5197593E-08 -1.9254140E-08 gauss-seidel spectral radius is 0.9869896 estimated iterations to convergence 72 setup time was (sec) 0.4600000 now iterating at: 08:54:25 rms-change max change #iterations 0.1420768 21.90010 at 10iterations 1.3803977E-02 1.982590 at 20iterations 1.3369928E-03 0.1760249 at 30iterations 1.5122198E-04 2.8257370E-02 at 40iterations 3.3919503E-05 6.7005157E-03 at 50iterations finished qdiffx linear iterations at : 08:54:28 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.3919503E-05 6.7005157E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 08:54:29 4.079u 0.260s 0:04.84 89.4% 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 08:54:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 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: 1.892007 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 1.892007 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 90.88227 91.28835 88.69278 assigned negative charge : -430.4511 centred at (gu) : 91.39671 91.23740 89.56475 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23336 grid for indexing accessible points = 1.400000 m= 27209 mr = 56260 m= 3719 mr = 19830 m= 176 mr = 2140 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2528 time to turn everything in is 0.4100000 number of dielectric boundary points 32488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20994 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) : 0.6306689 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5409250E-02 -8.4212959E-02 midg,1,midg; midg,igrid,midg -5.5958885E-03 -2.2071912E-03 1,midg,midg; igrid,midg,midg 5.6234282E-02 -1.6917735E-02 gauss-seidel spectral radius is 0.9986304 estimated iterations to convergence 214 setup time was (sec) 0.6600000 now iterating at: 08:54:30 rms-change max change #iterations 4.411602 170.7003 at 10iterations 2.072330 67.66972 at 20iterations 0.9714786 30.67055 at 30iterations 0.4565669 15.41883 at 40iterations 0.2135945 6.631703 at 50iterations 0.1005596 2.957602 at 60iterations 4.7001965E-02 1.524408 at 70iterations 2.2120547E-02 0.6736302 at 80iterations 1.0396445E-02 0.2923546 at 90iterations 4.8637106E-03 0.1509683 at 100iterations 2.2854505E-03 7.7273846E-02 at 110iterations 1.0779449E-03 3.4824371E-02 at 120iterations finished qdiffx linear iterations at : 08:54:38 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 1.0779449E-03 3.4824371E-02 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 08:54:39 8.665u 0.275s 0:09.78 91.3% 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 08:54:39 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 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: 2.838010 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 2.838010 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999833 assigned positive charge : 429.9503 centred at (gu) : 91.32342 91.93240 88.03891 assigned negative charge : -430.4511 centred at (gu) : 92.09496 91.85599 89.34692 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23336 grid for indexing accessible points = 1.400000 m= 90416 mr = 136415 m= 30247 mr = 73794 m= 6508 mr = 23880 m= 741 mr = 4646 m= 23 mr = 417 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 8598 time to turn everything in is 1.060000 number of dielectric boundary points 73242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 21352 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) : 1.892007 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2218931 -1.130297 midg,1,midg; midg,igrid,midg -0.1697327 -0.1415454 1,midg,midg; igrid,midg,midg 0.4633562 -0.4242595 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 1.340000 now iterating at: 08:54:40 rms-change max change #iterations 10.40201 300.3409 at 10iterations 6.133720 154.0802 at 20iterations 3.593831 77.25563 at 30iterations 2.096271 39.97165 at 40iterations 1.218282 25.67680 at 50iterations 0.7078649 14.51768 at 60iterations 0.4104826 7.630122 at 70iterations 0.2373024 4.279446 at 80iterations 0.1370245 2.445667 at 90iterations 7.9102114E-02 1.408585 at 100iterations 4.5667853E-02 0.8593349 at 110iterations 2.6337277E-02 0.5271950 at 120iterations 1.5181744E-02 0.2692623 at 130iterations 8.7710489E-03 0.1505489 at 140iterations 5.0536292E-03 9.4543457E-02 at 150iterations 2.9220849E-03 5.2339554E-02 at 160iterations 1.6933192E-03 3.2936096E-02 at 170iterations 9.8859554E-04 1.8623352E-02 at 180iterations finished qdiffx linear iterations at : 08:54:54 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 9.8859554E-04 1.8623352E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 08:54:57 15.487u 0.338s 0:18.00 87.8% 0+0k 0+0io 0pf+0w