Sun Oct 9 15:54:41 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 15:54:41 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 = 5587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4964509 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 0.4964509 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5413 net assigned charge : -1.999956 assigned positive charge : 860.4803 centred at (gu) : 89.11811 89.56617 89.18463 assigned negative charge : -862.4880 centred at (gu) : 89.09651 89.64180 89.12863 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8763 nv = 96 ne = 84 npr = 110304 no. pairs analyzed = 110304 no. exposed pairs = 6864 no. arc points = 47139 no. surface atoms = 2283 nbur = 3304 mkacc time = 0.1900000 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 = 1.708000 m= 298 mr = 4674 m= 2 mr = 6 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 0.3700000 number of dielectric boundary points 4383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4505 ## 707 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3628634E-10 6.3231989E-11 midg,1,midg; midg,igrid,midg 1.2575806E-10 -1.2661881E-10 1,midg,midg; igrid,midg,midg -6.4303077E-11 1.7160528E-11 gauss-seidel spectral radius is 0.9793108 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 15:54:41 rms-change max change #iterations 6.2501490E-02 8.852004 at 10iterations 5.2902345E-03 0.7983608 at 20iterations 1.6722665E-03 0.2859573 at 30iterations 6.4867042E-04 0.1122208 at 40iterations 2.5255204E-04 4.3952942E-02 at 50iterations finished qdiffx linear iterations at : 15:54:44 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.5255204E-04 4.3952942E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 15:54:45 3.641u 0.172s 0:04.09 93.1% 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 15:54:45 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 = 5587 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: 1.489353 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 1.489353 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5413 net assigned charge : -1.999956 assigned positive charge : 860.4803 centred at (gu) : 87.35288 88.69660 87.55222 assigned negative charge : -862.4880 centred at (gu) : 87.28962 88.92530 87.38542 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47139 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 30877 mr = 70378 m= 2605 mr = 21082 m= 40 mr = 1031 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1048 time to turn everything in is 0.4800000 number of dielectric boundary points 41012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 40272 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) : 0.4964509 object centre at (A) : -69.21750 -23.34600 1.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1171013E-02 5.0854622E-03 midg,1,midg; midg,igrid,midg 1.3705746E-02 -8.1807338E-03 1,midg,midg; igrid,midg,midg -3.6642935E-02 4.6163239E-03 gauss-seidel spectral radius is 0.9980588 estimated iterations to convergence 180 setup time was (sec) 0.7100000 now iterating at: 15:54:46 rms-change max change #iterations 3.951895 146.8661 at 10iterations 1.597399 58.51754 at 20iterations 0.6531533 22.63557 at 30iterations 0.2636678 7.616310 at 40iterations 0.1075139 3.487667 at 50iterations 4.4193756E-02 1.367153 at 60iterations 1.8599747E-02 0.6196556 at 70iterations 8.2903877E-03 0.2876434 at 80iterations 4.1614389E-03 0.1560593 at 90iterations 2.4376384E-03 9.0736389E-02 at 100iterations 1.6038454E-03 6.0031891E-02 at 110iterations 1.1175490E-03 4.1130066E-02 at 120iterations finished qdiffx linear iterations at : 15:54:53 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.1175490E-03 4.1130066E-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) 8.020000 DelPhi exited at 15:54:53 8.024u 0.194s 0:08.52 96.3% 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 Sun Oct 9 2011 at 15:54:53 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 = 5587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.234029 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 2.234029 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5413 net assigned charge : -1.999956 assigned positive charge : 860.4803 centred at (gu) : 86.02882 88.04459 86.32804 assigned negative charge : -862.4880 centred at (gu) : 85.93428 88.38781 86.07806 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 233220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47139 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 109282 mr = 172431 m= 28531 mr = 86670 m= 3579 mr = 20923 m= 126 mr = 2053 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 3607 time to turn everything in is 1.190000 number of dielectric boundary points 92646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 43150 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) : 1.489353 object centre at (A) : -69.21750 -23.34600 1.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5260375 0.1184497 midg,1,midg; midg,igrid,midg 0.3830708 -0.1411805 1,midg,midg; igrid,midg,midg -0.8952244 0.1777901 gauss-seidel spectral radius is 0.9991584 estimated iterations to convergence 272 setup time was (sec) 1.440000 now iterating at: 15:54:55 rms-change max change #iterations 10.90118 310.7311 at 10iterations 6.231714 136.2874 at 20iterations 3.537475 82.06705 at 30iterations 1.992421 47.82949 at 40iterations 1.117906 28.67813 at 50iterations 0.6251582 13.24512 at 60iterations 0.3497195 6.902180 at 70iterations 0.1950536 3.976868 at 80iterations 0.1089492 2.296246 at 90iterations 6.0459111E-02 1.143814 at 100iterations 3.3593804E-02 0.6138077 at 110iterations 1.8681353E-02 0.3575935 at 120iterations 1.0394515E-02 0.1931000 at 130iterations 5.8068065E-03 0.1124134 at 140iterations 3.2609312E-03 5.9700012E-02 at 150iterations 1.8495156E-03 3.4890175E-02 at 160iterations 1.0755374E-03 2.0214081E-02 at 170iterations 6.4905232E-04 1.3885498E-02 at 180iterations finished qdiffx linear iterations at : 15:55:07 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 6.4905232E-04 1.3885498E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 15:55:07 13.347u 0.210s 0:13.83 97.9% 0+0k 0+0io 0pf+0w