Mon Oct 10 13:55:11 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 Mon Oct 10 2011 at 13:55:11 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 = 3333 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: 0.5683451 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 0.5683451 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500013 assigned positive charge : 505.2205 centred at (gu) : 89.83133 89.85941 89.46949 assigned negative charge : -499.7218 centred at (gu) : 89.92642 89.84961 89.45075 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7330 nv = 96 ne = 84 npr = 64429 no. pairs analyzed = 64429 no. exposed pairs = 4500 no. arc points = 33328 no. surface atoms = 1479 nbur = 1854 mkacc time = 0.1100000 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 = 1.512000 m= 337 mr = 3572 m= 0 mr = 29 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3425 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4205518E-10 9.7785835E-10 midg,1,midg; midg,igrid,midg 6.5153438E-10 9.2739050E-10 1,midg,midg; igrid,midg,midg 2.4614890E-09 -7.7711171E-10 gauss-seidel spectral radius is 0.9840701 estimated iterations to convergence 65 setup time was (sec) 0.4200000 now iterating at: 13:55:11 rms-change max change #iterations 9.5486775E-02 16.32317 at 10iterations 6.9805505E-03 1.069550 at 20iterations 5.2643678E-04 7.6272011E-02 at 30iterations 3.8560327E-05 5.7716370E-03 at 40iterations 2.9523767E-06 4.3296814E-04 at 50iterations finished qdiffx linear iterations at : 13:55:14 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.9523767E-06 4.3296814E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 13:55:15 3.440u 0.180s 0:04.13 87.6% 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 Mon Oct 10 2011 at 13:55:16 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 = 3333 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: 1.705035 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 1.705035 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500013 assigned positive charge : 505.2205 centred at (gu) : 89.49309 89.57731 88.40758 assigned negative charge : -499.7218 centred at (gu) : 89.77893 89.54829 88.35168 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33328 grid for indexing accessible points = 1.400000 m= 25059 mr = 52807 m= 2986 mr = 16718 m= 130 mr = 1475 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1832 time to turn everything in is 0.3900000 number of dielectric boundary points 37385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24624 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) : 0.5683451 object centre at (A) : -26.26550 12.80200 -40.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3964280E-02 1.3875973E-02 midg,1,midg; midg,igrid,midg -1.4171867E-02 2.6542645E-02 1,midg,midg; igrid,midg,midg 3.8568000E-03 2.2809247E-03 gauss-seidel spectral radius is 0.9984047 estimated iterations to convergence 199 setup time was (sec) 0.6400000 now iterating at: 13:55:17 rms-change max change #iterations 3.896204 152.4401 at 10iterations 1.705145 57.55094 at 20iterations 0.7501550 23.79134 at 30iterations 0.3300336 10.35395 at 40iterations 0.1448265 4.721786 at 50iterations 6.3734040E-02 2.040470 at 60iterations 2.8029749E-02 0.9615214 at 70iterations 1.2338290E-02 0.4268723 at 80iterations 5.4086917E-03 0.1778488 at 90iterations 2.3895446E-03 7.5195313E-02 at 100iterations 1.0506761E-03 3.7605286E-02 at 110iterations 4.6353810E-04 1.6206741E-02 at 120iterations finished qdiffx linear iterations at : 13:55:24 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 4.6353810E-04 1.6206741E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 13:55:25 8.003u 0.269s 0:08.62 95.8% 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 Mon Oct 10 2011 at 13:55:25 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 = 3333 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: 2.557553 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): -54.70800 2.177000 ymin,ymax (A): -18.51700 44.12100 zmin,zma (A): -67.14000 -13.12200 x,y,z range (A): 56.88500 62.63800 54.01800 scale (grids/A): 2.557553 object centre (A): -26.26550 12.80200 -40.13100 number of atom coordinates read : 3333 total number of charged atoms : 3184 net assigned charge : 5.500013 assigned positive charge : 505.2205 centred at (gu) : 89.23927 89.36578 87.61101 assigned negative charge : -499.7218 centred at (gu) : 89.66827 89.32236 87.52738 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 185778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33328 grid for indexing accessible points = 1.400000 m= 85576 mr = 129441 m= 25390 mr = 66379 m= 4809 mr = 18432 m= 443 mr = 3142 m= 7 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 6305 time to turn everything in is 0.9600000 number of dielectric boundary points 84357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 25457 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) : 1.705035 object centre at (A) : -26.26550 12.80200 -40.13100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2319086 0.2389429 midg,1,midg; midg,igrid,midg -0.4633452 0.4013241 1,midg,midg; igrid,midg,midg 2.6525786E-02 1.9638315E-02 gauss-seidel spectral radius is 0.9992266 estimated iterations to convergence 284 setup time was (sec) 1.200000 now iterating at: 13:55:26 rms-change max change #iterations 9.902990 285.9201 at 10iterations 5.803719 203.9600 at 20iterations 3.380897 86.10155 at 30iterations 1.955242 42.24854 at 40iterations 1.125294 25.89488 at 50iterations 0.6461415 15.60953 at 60iterations 0.3701522 7.464652 at 70iterations 0.2115579 3.959015 at 80iterations 0.1208528 2.224131 at 90iterations 6.8934910E-02 1.271702 at 100iterations 3.9175473E-02 0.8091240 at 110iterations 2.2299426E-02 0.4064770 at 120iterations 1.2684589E-02 0.2428150 at 130iterations 7.1986923E-03 0.1318755 at 140iterations 4.1029225E-03 9.1676235E-02 at 150iterations 2.3264347E-03 4.4128418E-02 at 160iterations 1.3236904E-03 2.5482178E-02 at 170iterations 7.5113983E-04 1.4829636E-02 at 180iterations finished qdiffx linear iterations at : 13:55:38 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 7.5113983E-04 1.4829636E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 13:55:39 12.943u 0.227s 0:14.22 92.5% 0+0k 0+0io 0pf+0w