Sun Oct 9 07:23:06 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+sph2.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 = amb2.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 07:23:06 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2531 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: 0.5457612 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): -5.372000 41.19600 ymin,ymax (A): 35.28800 87.26800 zmin,zma (A): -3.479000 61.75100 x,y,z range (A): 46.56800 51.98000 65.23000 scale (grids/A): 0.5457612 object centre (A): 17.91200 61.27800 29.13600 number of atom coordinates read : 2531 total number of charged atoms : 2386 net assigned charge : -11.49998 assigned positive charge : 379.6528 centred at (gu) : 91.08936 89.08533 89.77767 assigned negative charge : -391.1533 centred at (gu) : 91.26135 88.72208 89.72453 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4949 nv = 96 ne = 84 npr = 50827 no. pairs analyzed = 50827 no. exposed pairs = 3543 no. arc points = 25069 no. surface atoms = 1177 nbur = 1354 mkacc time = 0.1400000 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 = 1.568000 m= 190 mr = 2343 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2477 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6422 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0323481E-09 -3.4560937E-10 midg,1,midg; midg,igrid,midg -3.6064418E-09 1.0581880E-09 1,midg,midg; igrid,midg,midg 2.2480198E-10 -2.2089217E-09 gauss-seidel spectral radius is 0.9826626 estimated iterations to convergence 63 setup time was (sec) 0.6100000 now iterating at: 07:23:07 rms-change max change #iterations 6.7052580E-02 12.45429 at 10iterations 4.3919235E-03 0.7917938 at 20iterations 2.8816008E-04 5.5970192E-02 at 30iterations 1.9233386E-05 3.4966469E-03 at 40iterations 1.3921397E-06 2.3651123E-04 at 50iterations finished qdiffx linear iterations at : 07:23:10 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.3921397E-06 2.3651123E-04 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 07:23:11 4.062u 0.251s 0:04.57 94.3% 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 07:23:11 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2531 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: 1.637284 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): -5.372000 41.19600 ymin,ymax (A): 35.28800 87.26800 zmin,zma (A): -3.479000 61.75100 x,y,z range (A): 46.56800 51.98000 65.23000 scale (grids/A): 1.637284 object centre (A): 17.91200 61.27800 29.13600 number of atom coordinates read : 2531 total number of charged atoms : 2386 net assigned charge : -11.49998 assigned positive charge : 379.6528 centred at (gu) : 93.26772 87.25551 89.33228 assigned negative charge : -391.1533 centred at (gu) : 93.78378 86.16595 89.17326 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 54213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25069 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15869 mr = 34466 m= 1391 mr = 10517 m= 30 mr = 559 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.5100000 number of dielectric boundary points 25961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18263 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) : 0.5457612 object centre at (A) : 17.91200 61.27800 29.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1543709E-02 -9.2699821E-04 midg,1,midg; midg,igrid,midg -2.3123961E-02 7.1771294E-03 1,midg,midg; igrid,midg,midg -2.4346809E-03 -1.8700413E-02 gauss-seidel spectral radius is 0.9981472 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 07:23:12 rms-change max change #iterations 3.071363 143.2509 at 10iterations 1.266739 59.98109 at 20iterations 0.5202152 22.67904 at 30iterations 0.2140297 9.450029 at 40iterations 8.8286392E-02 3.951324 at 50iterations 3.6485877E-02 1.374519 at 60iterations 1.5025537E-02 0.5940628 at 70iterations 6.2032021E-03 0.2667255 at 80iterations 2.5576509E-03 9.9777222E-02 at 90iterations 1.0537951E-03 4.3373108E-02 at 100iterations 4.3552605E-04 1.8211365E-02 at 110iterations 1.7972974E-04 6.8368912E-03 at 120iterations finished qdiffx linear iterations at : 07:23:20 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 1.7972974E-04 6.8368912E-03 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 07:23:20 9.066u 0.310s 0:09.66 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 Sun Oct 9 2011 at 07:23:20 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2531 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: 2.455925 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): -5.372000 41.19600 ymin,ymax (A): 35.28800 87.26800 zmin,zma (A): -3.479000 61.75100 x,y,z range (A): 46.56800 51.98000 65.23000 scale (grids/A): 2.455925 object centre (A): 17.91200 61.27800 29.13600 number of atom coordinates read : 2531 total number of charged atoms : 2386 net assigned charge : -11.49998 assigned positive charge : 379.6528 centred at (gu) : 94.90147 85.88300 88.99832 assigned negative charge : -391.1533 centred at (gu) : 95.67551 84.24876 88.75974 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 125863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25069 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55750 mr = 84869 m= 14297 mr = 42930 m= 2009 mr = 10362 m= 108 mr = 1141 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 275 time to turn everything in is 1.180000 number of dielectric boundary points 58685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 19062 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) : 1.637284 object centre at (A) : 17.91200 61.27800 29.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7885771 -1.9848617E-02 midg,1,midg; midg,igrid,midg -0.3020454 9.8618746E-02 1,midg,midg; igrid,midg,midg -3.6803704E-02 -0.2343955 gauss-seidel spectral radius is 0.9991183 estimated iterations to convergence 266 setup time was (sec) 1.500000 now iterating at: 07:23:22 rms-change max change #iterations 8.030372 310.9817 at 10iterations 4.436335 115.0909 at 20iterations 2.472313 61.61054 at 30iterations 1.363225 33.02075 at 40iterations 0.7502283 18.37768 at 50iterations 0.4143397 9.820208 at 60iterations 0.2269345 5.728003 at 70iterations 0.1243848 2.852935 at 80iterations 6.7921780E-02 1.618385 at 90iterations 3.7106313E-02 0.8116093 at 100iterations 2.0333892E-02 0.4800321 at 110iterations 1.1080283E-02 0.2682003 at 120iterations 6.0499189E-03 0.1332436 at 130iterations 3.2957122E-03 7.6624870E-02 at 140iterations 1.8015539E-03 3.9471626E-02 at 150iterations 9.8439946E-04 2.1935463E-02 at 160iterations 5.3728081E-04 1.1716843E-02 at 170iterations 2.9262851E-04 6.5155029E-03 at 180iterations finished qdiffx linear iterations at : 07:23:35 total time elapsed so far: 14.60000 # loops : 180 mean,max change (kT/e) : 2.9262851E-04 6.5155029E-03 energy calculations done at 14.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.77000 DelPhi exited at 07:23:36 14.775u 0.309s 0:15.34 98.2% 0+0k 0+0io 0pf+0w