Sat Oct 15 15:21:15 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 Sat Oct 15 2011 at 15:21:15 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6626585 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 0.6626585 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.154012 assigned positive charge : 427.8257 centred at (gu) : 89.73919 90.44054 91.13380 assigned negative charge : -425.6722 centred at (gu) : 89.49612 90.28089 91.08975 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8297 nv = 96 ne = 84 npr = 56389 no. pairs analyzed = 56389 no. exposed pairs = 3471 no. arc points = 23954 no. surface atoms = 1166 nbur = 1632 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4705 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2100000 number of dielectric boundary points 4004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2326 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4273027E-09 2.0285592E-08 midg,1,midg; midg,igrid,midg -2.8972790E-08 4.6359276E-08 1,midg,midg; igrid,midg,midg -5.5011622E-08 5.7564169E-08 gauss-seidel spectral radius is 0.9882118 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 15:21:16 rms-change max change #iterations 0.1769876 25.87428 at 10iterations 1.9243393E-02 3.419171 at 20iterations 2.1400023E-03 0.2573624 at 30iterations 2.7502261E-04 3.9581299E-02 at 40iterations 5.0878472E-05 6.0749054E-03 at 50iterations finished qdiffx linear iterations at : 15:21:19 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.0878472E-05 6.0749054E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 15:21:19 3.493u 0.185s 0:03.99 91.9% 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 15:21:19 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.987975 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 1.987975 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.154012 assigned positive charge : 427.8257 centred at (gu) : 89.21680 91.32115 93.40073 assigned negative charge : -425.6722 centred at (gu) : 88.48839 90.84219 93.26885 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 33240 mr = 63033 m= 5485 mr = 24883 m= 373 mr = 3379 m= 10 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 757 time to turn everything in is 0.4500000 number of dielectric boundary points 36722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 20926 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) : 0.6626585 object centre at (A) : 13.67950 -1.363000 18.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3403324E-02 8.8656731E-03 midg,1,midg; midg,igrid,midg -1.8093321E-02 9.8899314E-03 1,midg,midg; igrid,midg,midg -1.9739257E-02 7.5931184E-02 gauss-seidel spectral radius is 0.9987620 estimated iterations to convergence 225 setup time was (sec) 0.6800000 now iterating at: 15:21:20 rms-change max change #iterations 4.910790 223.9622 at 10iterations 2.396393 68.99203 at 20iterations 1.156803 37.09890 at 30iterations 0.5633112 16.89400 at 40iterations 0.2740392 9.076368 at 50iterations 0.1331122 3.932794 at 60iterations 6.4665206E-02 1.947357 at 70iterations 3.1580474E-02 0.9610367 at 80iterations 1.5334628E-02 0.4965343 at 90iterations 7.4584116E-03 0.2016869 at 100iterations 3.6361166E-03 9.8365307E-02 at 110iterations 1.7702669E-03 5.3056717E-02 at 120iterations finished qdiffx linear iterations at : 15:21:28 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 1.7702669E-03 5.3056717E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 15:21:28 8.226u 0.212s 0:08.86 95.1% 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 15:21:28 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.981963 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 2.981963 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.154012 assigned positive charge : 427.8257 centred at (gu) : 88.82516 91.98158 95.10112 assigned negative charge : -425.6722 centred at (gu) : 87.73248 91.26323 94.90306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 205393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 107196 mr = 152101 m= 39834 mr = 88544 m= 9970 mr = 32187 m= 1579 mr = 7339 m= 110 mr = 1055 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2765 time to turn everything in is 1.150000 number of dielectric boundary points 82810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 21158 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) : 1.987975 object centre at (A) : 13.67950 -1.363000 18.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9766696 0.2780803 midg,1,midg; midg,igrid,midg -0.2098390 5.4702833E-02 1,midg,midg; igrid,midg,midg -0.1487437 0.6391540 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 15:21:30 rms-change max change #iterations 11.25279 430.7471 at 10iterations 6.643023 137.1681 at 20iterations 3.907872 76.83339 at 30iterations 2.299258 43.42604 at 40iterations 1.351250 24.04475 at 50iterations 0.7904513 14.97799 at 60iterations 0.4640948 9.087229 at 70iterations 0.2713834 4.887251 at 80iterations 0.1585132 2.726782 at 90iterations 9.2548661E-02 1.603933 at 100iterations 5.4136507E-02 0.9213512 at 110iterations 3.1592369E-02 0.5319386 at 120iterations 1.8428268E-02 0.2979174 at 130iterations 1.0786585E-02 0.1840286 at 140iterations 6.3083638E-03 0.1055470 at 150iterations 3.7110606E-03 6.1990738E-02 at 160iterations 2.1921247E-03 3.9482594E-02 at 170iterations 1.3077765E-03 2.1435738E-02 at 180iterations finished qdiffx linear iterations at : 15:21:42 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 1.3077765E-03 2.1435738E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 15:21:43 13.710u 0.241s 0:14.24 97.9% 0+0k 0+0io 0pf+0w