Tue Oct 11 08:25:53 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 Tue Oct 11 2011 at 08:25:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6617346 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 0.6617346 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.162028 assigned positive charge : 404.6859 centred at (gu) : 90.71035 90.69755 91.35169 assigned negative charge : -400.5245 centred at (gu) : 90.42988 90.47286 91.25195 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7904 nv = 96 ne = 84 npr = 54725 no. pairs analyzed = 54725 no. exposed pairs = 3231 no. arc points = 22401 no. surface atoms = 1086 nbur = 1601 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4541 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.3000000 number of dielectric boundary points 3764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2225 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9345 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4696481E-09 4.1245471E-08 midg,1,midg; midg,igrid,midg -3.3566295E-08 6.5780874E-08 1,midg,midg; igrid,midg,midg -4.4266244E-08 7.9061692E-08 gauss-seidel spectral radius is 0.9881681 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 08:25:54 rms-change max change #iterations 0.1742749 22.13679 at 10iterations 1.8904410E-02 2.381077 at 20iterations 2.0479870E-03 0.2601671 at 30iterations 2.2123958E-04 3.0105591E-02 at 40iterations 2.5241297E-05 3.2629967E-03 at 50iterations finished qdiffx linear iterations at : 08:25:58 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 2.5241297E-05 3.2629967E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 08:25:58 4.037u 0.353s 0:04.69 93.3% 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 Tue Oct 11 2011 at 08:25:58 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.985204 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 1.985204 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.162028 assigned positive charge : 404.6859 centred at (gu) : 92.13071 92.09206 94.05469 assigned negative charge : -400.5245 centred at (gu) : 91.28927 91.41850 93.75579 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 83989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22401 grid for indexing accessible points = 1.400000 m= 33443 mr = 59507 m= 6062 mr = 25597 m= 451 mr = 4083 m= 6 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2300 time to turn everything in is 0.8000000 number of dielectric boundary points 34598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20027 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) : 0.6617346 object centre at (A) : 11.75000 -3.362000 18.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8538713E-02 6.3449410E-03 midg,1,midg; midg,igrid,midg -1.3194033E-02 5.3487539E-02 1,midg,midg; igrid,midg,midg -1.5219715E-02 8.7127864E-02 gauss-seidel spectral radius is 0.9987452 estimated iterations to convergence 224 setup time was (sec) 1.100000 now iterating at: 08:26:00 rms-change max change #iterations 4.667120 197.0701 at 10iterations 2.266153 82.70508 at 20iterations 1.091408 35.12865 at 30iterations 0.5300924 15.24973 at 40iterations 0.2568335 7.587532 at 50iterations 0.1244514 4.578060 at 60iterations 6.0362663E-02 1.770133 at 70iterations 2.9170975E-02 0.9098225 at 80iterations 1.4119345E-02 0.3964983 at 90iterations 6.8361936E-03 0.2218304 at 100iterations 3.3153936E-03 9.5596313E-02 at 110iterations 1.6142495E-03 4.8486710E-02 at 120iterations finished qdiffx linear iterations at : 08:26:08 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 1.6142495E-03 4.8486710E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.990000 DelPhi exited at 08:26:09 9.996u 0.403s 0:10.72 96.9% 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 Tue Oct 11 2011 at 08:26:09 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.977806 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 2.977806 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.162028 assigned positive charge : 404.6859 centred at (gu) : 93.19582 93.13795 96.08188 assigned negative charge : -400.5245 centred at (gu) : 91.93386 92.12762 95.63359 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 193918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22401 grid for indexing accessible points = 1.400000 m= 104674 mr = 143399 m= 42098 mr = 87421 m= 11192 mr = 34948 m= 1824 mr = 8663 m= 140 mr = 1311 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 7741 time to turn everything in is 1.800000 number of dielectric boundary points 78042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 20282 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) : 1.985204 object centre at (A) : 11.75000 -3.362000 18.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7090175 0.1731408 midg,1,midg; midg,igrid,midg -0.1531762 0.5757179 1,midg,midg; igrid,midg,midg -0.1702901 0.7421508 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 2.210000 now iterating at: 08:26:12 rms-change max change #iterations 10.77890 419.2972 at 10iterations 6.342720 163.9859 at 20iterations 3.729565 70.43124 at 30iterations 2.194633 47.61703 at 40iterations 1.281522 22.63799 at 50iterations 0.7508942 12.95759 at 60iterations 0.4382510 9.365778 at 70iterations 0.2558323 4.729928 at 80iterations 0.1495118 2.698124 at 90iterations 8.6997852E-02 1.568649 at 100iterations 5.0686106E-02 0.8297005 at 110iterations 2.9437499E-02 0.4996529 at 120iterations 1.7159441E-02 0.2780666 at 130iterations 9.9655176E-03 0.1737900 at 140iterations 5.8254167E-03 9.5750809E-02 at 150iterations 3.3981716E-03 5.7434082E-02 at 160iterations 1.9921993E-03 3.1521082E-02 at 170iterations 1.1723407E-03 1.9867897E-02 at 180iterations finished qdiffx linear iterations at : 08:26:27 total time elapsed so far: 17.12000 # loops : 180 mean,max change (kT/e) : 1.1723407E-03 1.9867897E-02 energy calculations done at 17.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.30000 DelPhi exited at 08:26:27 17.301u 0.420s 0:18.08 98.0% 0+0k 0+0io 0pf+0w