Sat Oct 15 11:27:26 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 Sat Oct 15 2011 at 11:27:27 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 = 3517 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: 0.5061563 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): -13.11900 38.79400 ymin,ymax (A): -32.12700 38.20700 zmin,zma (A): 1.255000 50.01900 x,y,z range (A): 51.91300 70.33400 48.76400 scale (grids/A): 0.5061563 object centre (A): 12.83750 3.040001 25.63700 number of atom coordinates read : 3517 total number of charged atoms : 3372 net assigned charge : -4.499995 assigned positive charge : 525.4699 centred at (gu) : 90.19891 90.01772 90.17981 assigned negative charge : -529.9715 centred at (gu) : 90.22816 90.06754 90.17680 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5698 nv = 96 ne = 84 npr = 72237 no. pairs analyzed = 72237 no. exposed pairs = 4317 no. arc points = 29822 no. surface atoms = 1459 nbur = 2058 mkacc time = 0.1300000 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= 179 mr = 2976 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2927 ## 432 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7601 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4406674E-11 -4.9681224E-11 midg,1,midg; midg,igrid,midg 2.6395306E-11 -1.3265027E-10 1,midg,midg; igrid,midg,midg -5.6667201E-12 -1.0427196E-10 gauss-seidel spectral radius is 0.9799458 estimated iterations to convergence 58 setup time was (sec) 0.4900000 now iterating at: 11:27:27 rms-change max change #iterations 5.3253509E-02 9.331657 at 10iterations 2.9370126E-03 0.4819031 at 20iterations 2.1402835E-04 3.8280368E-02 at 30iterations 3.4094304E-05 7.2965622E-03 at 40iterations 7.3063716E-06 1.5764236E-03 at 50iterations finished qdiffx linear iterations at : 11:27:31 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 7.3063716E-06 1.5764236E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 11:27:32 3.876u 0.315s 0:05.58 74.9% 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 Sat Oct 15 2011 at 11:27:32 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 = 3517 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: 1.518469 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): -13.11900 38.79400 ymin,ymax (A): -32.12700 38.20700 zmin,zma (A): 1.255000 50.01900 x,y,z range (A): 51.91300 70.33400 48.76400 scale (grids/A): 1.518469 object centre (A): 12.83750 3.040001 25.63700 number of atom coordinates read : 3517 total number of charged atoms : 3372 net assigned charge : -4.499995 assigned positive charge : 525.4699 centred at (gu) : 90.59575 90.05190 90.53873 assigned negative charge : -529.9715 centred at (gu) : 90.68393 90.20207 90.52985 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 18066 mr = 43909 m= 1450 mr = 12072 m= 25 mr = 594 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.3200000 number of dielectric boundary points 26891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 25264 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) : 0.5061563 object centre at (A) : 12.83750 3.040001 25.63700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5749607E-03 -5.1866961E-03 midg,1,midg; midg,igrid,midg 1.4108564E-02 5.1681732E-04 1,midg,midg; igrid,midg,midg 2.2283716E-03 -2.5116040E-03 gauss-seidel spectral radius is 0.9979333 estimated iterations to convergence 175 setup time was (sec) 0.5400000 now iterating at: 11:27:33 rms-change max change #iterations 3.077998 162.6056 at 10iterations 1.205213 49.51340 at 20iterations 0.4764854 18.26528 at 30iterations 0.1873577 6.386888 at 40iterations 7.3665634E-02 3.307434 at 50iterations 2.9147886E-02 1.088326 at 60iterations 1.1495812E-02 0.4370670 at 70iterations 4.5603630E-03 0.1644011 at 80iterations 1.8148336E-03 7.5472832E-02 at 90iterations 7.4468099E-04 2.6779175E-02 at 100iterations 3.1116698E-04 1.3130069E-02 at 110iterations 1.4039576E-04 5.6991577E-03 at 120iterations finished qdiffx linear iterations at : 11:27:42 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 1.4039576E-04 5.6991577E-03 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 11:27:43 8.132u 0.242s 0:10.71 78.1% 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 Sat Oct 15 2011 at 11:27:43 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 = 3517 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: 2.277704 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): -13.11900 38.79400 ymin,ymax (A): -32.12700 38.20700 zmin,zma (A): 1.255000 50.01900 x,y,z range (A): 51.91300 70.33400 48.76400 scale (grids/A): 2.277704 object centre (A): 12.83750 3.040001 25.63700 number of atom coordinates read : 3517 total number of charged atoms : 3372 net assigned charge : -4.499995 assigned positive charge : 525.4699 centred at (gu) : 90.89327 90.07767 90.80788 assigned negative charge : -529.9715 centred at (gu) : 91.02560 90.30301 90.79471 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 148988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 65746 mr = 107846 m= 15833 mr = 51373 m= 1933 mr = 11409 m= 75 mr = 1174 m= 0 mr = 25 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 683 time to turn everything in is 0.7800000 number of dielectric boundary points 60748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 26886 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) : 1.518469 object centre at (A) : 12.83750 3.040001 25.63700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2240001E-02 -8.9787327E-02 midg,1,midg; midg,igrid,midg 0.5984837 0.1021605 1,midg,midg; igrid,midg,midg 5.9406627E-02 -3.8123667E-02 gauss-seidel spectral radius is 0.9990632 estimated iterations to convergence 258 setup time was (sec) 1.030000 now iterating at: 11:27:44 rms-change max change #iterations 8.303688 247.5768 at 10iterations 4.530125 118.0902 at 20iterations 2.451740 61.22090 at 30iterations 1.324094 30.16863 at 40iterations 0.7137084 15.85001 at 50iterations 0.3852710 9.314728 at 60iterations 0.2069717 4.405673 at 70iterations 0.1112048 2.396328 at 80iterations 5.9526455E-02 1.237129 at 90iterations 3.2029636E-02 0.7047319 at 100iterations 1.7174553E-02 0.3802986 at 110iterations 9.2216209E-03 0.1846743 at 120iterations 4.9408213E-03 9.9801064E-02 at 130iterations 2.6459659E-03 5.5187225E-02 at 140iterations 1.4275786E-03 3.2905579E-02 at 150iterations 7.6847064E-04 1.7221451E-02 at 160iterations 4.1411418E-04 9.0560913E-03 at 170iterations 2.2552654E-04 4.6300888E-03 at 180iterations finished qdiffx linear iterations at : 11:28:00 total time elapsed so far: 14.64000 # loops : 180 mean,max change (kT/e) : 2.2552654E-04 4.6300888E-03 energy calculations done at 14.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.77000 DelPhi exited at 11:28:01 14.774u 0.285s 0:18.06 83.3% 0+0k 0+0io 0pf+0w