Sun Oct 9 14:01:29 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 14:01:29 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 = 2376 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6754449 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 0.6754449 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 90.69086 90.69264 90.26737 assigned negative charge : -359.1295 centred at (gu) : 90.88055 90.64231 90.13461 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 47534 no. pairs analyzed = 47534 no. exposed pairs = 2982 no. arc points = 20825 no. surface atoms = 1007 nbur = 1369 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4074 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4973346E-08 4.7639158E-08 midg,1,midg; midg,igrid,midg -3.2269345E-09 2.6845962E-08 1,midg,midg; igrid,midg,midg 5.2000999E-08 -4.8962008E-08 gauss-seidel spectral radius is 0.9886173 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 14:01:30 rms-change max change #iterations 0.1789201 25.55938 at 10iterations 2.0059286E-02 2.987852 at 20iterations 2.6636033E-03 0.4560871 at 30iterations 5.3200917E-04 8.4228516E-02 at 40iterations 1.5139711E-04 2.4692535E-02 at 50iterations finished qdiffx linear iterations at : 14:01:32 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.5139711E-04 2.4692535E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:01:33 3.083u 0.135s 0:03.48 92.2% 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 14:01:33 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 = 2376 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.026335 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 2.026335 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 92.07213 92.07725 90.80160 assigned negative charge : -359.1295 centred at (gu) : 92.64114 91.92667 90.40363 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20825 grid for indexing accessible points = 1.400000 m= 29470 mr = 54647 m= 4981 mr = 21899 m= 350 mr = 3165 m= 9 mr = 150 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 33628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17679 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) : 0.6754449 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1741707E-03 6.7404926E-02 midg,1,midg; midg,igrid,midg 4.1976586E-02 5.0147060E-02 1,midg,midg; igrid,midg,midg 5.2644694E-03 -3.3523481E-02 gauss-seidel spectral radius is 0.9987703 estimated iterations to convergence 226 setup time was (sec) 0.8300000 now iterating at: 14:01:34 rms-change max change #iterations 4.598053 203.5989 at 10iterations 2.231033 73.63982 at 20iterations 1.091766 33.87902 at 30iterations 0.5298837 16.22738 at 40iterations 0.2573826 7.536716 at 50iterations 0.1254781 3.943206 at 60iterations 6.1405193E-02 1.968513 at 70iterations 3.0002292E-02 0.9171276 at 80iterations 1.4693628E-02 0.4617796 at 90iterations 7.2481744E-03 0.2316983 at 100iterations 3.6583908E-03 0.1072540 at 110iterations 1.8769285E-03 5.8568954E-02 at 120iterations finished qdiffx linear iterations at : 14:01:40 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.8769285E-03 5.8568954E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:01:40 6.990u 0.154s 0:07.46 95.7% 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 14:01:40 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 = 2376 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.039502 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 3.039502 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 361.6291 centred at (gu) : 93.10811 93.11574 91.20229 assigned negative charge : -359.1295 centred at (gu) : 93.96168 92.89008 90.60529 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 181895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20825 grid for indexing accessible points = 1.400000 m= 94397 mr = 132453 m= 35170 mr = 77504 m= 9040 mr = 28349 m= 1584 mr = 6881 m= 139 mr = 1134 m= 9 mr = 79 m= 0 mr = 4 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 75830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 17868 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) : 2.026335 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1812193E-02 0.8462379 midg,1,midg; midg,igrid,midg 1.185347 0.9832217 1,midg,midg; igrid,midg,midg 3.4159109E-02 -0.3757826 gauss-seidel spectral radius is 0.9992863 estimated iterations to convergence 295 setup time was (sec) 1.670000 now iterating at: 14:01:42 rms-change max change #iterations 10.47529 412.0931 at 10iterations 6.164322 132.9796 at 20iterations 3.630815 69.50816 at 30iterations 2.129567 39.14069 at 40iterations 1.246474 24.42349 at 50iterations 0.7290623 14.60996 at 60iterations 0.4257972 7.092472 at 70iterations 0.2486432 4.301903 at 80iterations 0.1449785 2.472301 at 90iterations 8.4553137E-02 1.700195 at 100iterations 4.9367756E-02 0.8482475 at 110iterations 2.8863095E-02 0.5065002 at 120iterations 1.6923647E-02 0.3025913 at 130iterations 1.0043579E-02 0.1975136 at 140iterations 6.0537872E-03 0.1183853 at 150iterations 3.7513096E-03 7.7993393E-02 at 160iterations 2.4297247E-03 5.3970337E-02 at 170iterations 1.6707341E-03 4.0416718E-02 at 180iterations finished qdiffx linear iterations at : 14:01:52 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 1.6707341E-03 4.0416718E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 14:01:52 11.324u 0.163s 0:11.80 97.2% 0+0k 0+0io 0pf+0w