Sun Oct 9 16:09:12 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 16:09:12 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 = 3066 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: 0.6319901 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 0.6319901 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2922 net assigned charge : -6.499975 assigned positive charge : 452.2190 centred at (gu) : 90.39513 91.19910 88.76285 assigned negative charge : -458.7205 centred at (gu) : 90.39895 91.33661 88.69349 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8201 nv = 96 ne = 84 npr = 63105 no. pairs analyzed = 63105 no. exposed pairs = 3747 no. arc points = 26422 no. surface atoms = 1276 nbur = 1790 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4546 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9405483E-08 2.4707464E-10 midg,1,midg; midg,igrid,midg 5.8938681E-09 -2.9273602E-08 1,midg,midg; igrid,midg,midg -6.1996368E-09 -8.2221119E-09 gauss-seidel spectral radius is 0.9870718 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 16:09:12 rms-change max change #iterations 0.1510707 19.31570 at 10iterations 1.4621639E-02 1.931458 at 20iterations 1.4222781E-03 0.1948166 at 30iterations 1.5013656E-04 2.1329880E-02 at 40iterations 2.3779074E-05 3.4751892E-03 at 50iterations finished qdiffx linear iterations at : 16:09:15 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.3779074E-05 3.4751892E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 16:09:16 3.408u 0.196s 0:03.96 90.6% 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 Sun Oct 9 2011 at 16:09:16 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 = 3066 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: 1.895970 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 1.895970 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2922 net assigned charge : -6.499975 assigned positive charge : 452.2190 centred at (gu) : 91.18466 93.59653 86.28788 assigned negative charge : -458.7205 centred at (gu) : 91.19682 94.00931 86.08008 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 32352 mr = 62321 m= 5703 mr = 23558 m= 365 mr = 3558 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 22982 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) : 0.6319901 object centre at (A) : 10.79050 29.96250 -6.659999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1263033E-02 1.7656922E-02 midg,1,midg; midg,igrid,midg -1.9451495E-02 -4.0800244E-02 1,midg,midg; igrid,midg,midg -3.1835765E-02 -2.9502764E-02 gauss-seidel spectral radius is 0.9986660 estimated iterations to convergence 217 setup time was (sec) 0.6600000 now iterating at: 16:09:16 rms-change max change #iterations 4.618844 191.2742 at 10iterations 2.176935 75.46715 at 20iterations 1.033078 31.07850 at 30iterations 0.4859182 15.01322 at 40iterations 0.2292344 6.875214 at 50iterations 0.1084502 3.156105 at 60iterations 5.1362555E-02 1.642389 at 70iterations 2.4255957E-02 0.6666069 at 80iterations 1.1457367E-02 0.3436579 at 90iterations 5.4440554E-03 0.1540909 at 100iterations 2.5905690E-03 7.8716278E-02 at 110iterations 1.2484924E-03 3.8148880E-02 at 120iterations finished qdiffx linear iterations at : 16:09:23 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.2484924E-03 3.8148880E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 16:09:24 7.860u 0.184s 0:08.30 96.8% 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 Sun Oct 9 2011 at 16:09:24 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 = 3066 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: 2.843956 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 2.843956 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2922 net assigned charge : -6.499975 assigned positive charge : 452.2190 centred at (gu) : 91.77664 95.39445 84.43150 assigned negative charge : -458.7205 centred at (gu) : 91.79518 96.01398 84.11997 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 206007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 103713 mr = 151385 m= 38991 mr = 84409 m= 10326 mr = 30877 m= 1543 mr = 7778 m= 100 mr = 1001 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 85189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 23374 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) : 1.895970 object centre at (A) : 10.79050 29.96250 -6.659999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9239946E-02 0.3580787 midg,1,midg; midg,igrid,midg -0.3445566 -0.4056051 1,midg,midg; igrid,midg,midg -0.4155408 -0.3189145 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 1.350000 now iterating at: 16:09:25 rms-change max change #iterations 10.89855 504.0015 at 10iterations 6.457061 138.7477 at 20iterations 3.801929 76.27577 at 30iterations 2.227824 42.28727 at 40iterations 1.307323 23.78921 at 50iterations 0.7635538 14.74684 at 60iterations 0.4459416 8.555187 at 70iterations 0.2596048 4.681257 at 80iterations 0.1511092 3.206116 at 90iterations 8.7684497E-02 1.641657 at 100iterations 5.0922308E-02 0.8523865 at 110iterations 2.9638389E-02 0.5838165 at 120iterations 1.7203629E-02 0.3153868 at 130iterations 9.9933315E-03 0.1672516 at 140iterations 5.7925708E-03 0.1016017 at 150iterations 3.3627867E-03 6.4403534E-02 at 160iterations 1.9495598E-03 3.3233166E-02 at 170iterations 1.1362493E-03 2.0942688E-02 at 180iterations finished qdiffx linear iterations at : 16:09:37 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.1362493E-03 2.0942688E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 16:09:37 13.021u 0.213s 0:13.50 98.0% 0+0k 0+0io 0pf+0w