Mon Oct 10 23:52:29 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 Mon Oct 10 2011 at 23:52:29 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6166958 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 0.6166958 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2453 net assigned charge : 8.906025 assigned positive charge : 390.7289 centred at (gu) : 88.74843 91.56543 89.47467 assigned negative charge : -381.8235 centred at (gu) : 88.73537 91.38718 89.63347 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 52685 no. pairs analyzed = 52685 no. exposed pairs = 3105 no. arc points = 21675 no. surface atoms = 1054 nbur = 1543 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3638 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3100000 number of dielectric boundary points 3156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8088 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7372292E-08 -2.9207214E-09 midg,1,midg; midg,igrid,midg -3.1014260E-09 2.3499418E-08 1,midg,midg; igrid,midg,midg 7.1350512E-09 5.3669806E-09 gauss-seidel spectral radius is 0.9863805 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 23:52:30 rms-change max change #iterations 0.1247155 20.06085 at 10iterations 1.2420701E-02 1.898659 at 20iterations 1.6727311E-03 0.3357086 at 30iterations 4.0728869E-04 9.5489502E-02 at 40iterations 1.1919431E-04 2.8686523E-02 at 50iterations finished qdiffx linear iterations at : 23:52:33 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.1919431E-04 2.8686523E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 23:52:33 3.654u 0.208s 0:04.19 91.8% 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 23:52:33 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.850087 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 1.850087 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2453 net assigned charge : 8.906025 assigned positive charge : 390.7289 centred at (gu) : 86.24467 94.69576 88.42337 assigned negative charge : -381.8235 centred at (gu) : 86.20580 94.16136 88.90005 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21675 grid for indexing accessible points = 1.400000 m= 24840 mr = 49413 m= 3597 mr = 18289 m= 141 mr = 2225 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1098 time to turn everything in is 0.5900000 number of dielectric boundary points 29252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19239 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) : 0.6166958 object centre at (A) : 37.42050 27.51650 32.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6349289E-02 3.7417074E-03 midg,1,midg; midg,igrid,midg -1.3762183E-02 2.1549126E-02 1,midg,midg; igrid,midg,midg -2.0891868E-03 1.7502157E-02 gauss-seidel spectral radius is 0.9985495 estimated iterations to convergence 208 setup time was (sec) 0.9000000 now iterating at: 23:52:34 rms-change max change #iterations 4.001849 166.2201 at 10iterations 1.823495 64.86047 at 20iterations 0.8320343 29.08438 at 30iterations 0.3813394 12.34841 at 40iterations 0.1749583 5.659329 at 50iterations 8.0262914E-02 2.729952 at 60iterations 3.6889322E-02 1.158625 at 70iterations 1.6982596E-02 0.5297852 at 80iterations 7.9918252E-03 0.2757747 at 90iterations 3.7870295E-03 0.1349716 at 100iterations 1.8784263E-03 6.9118500E-02 at 110iterations 9.9335716E-04 4.0531158E-02 at 120iterations finished qdiffx linear iterations at : 23:52:41 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 9.9335716E-04 4.0531158E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 23:52:42 8.148u 0.248s 0:08.69 96.4% 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 23:52:42 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.775131 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 2.775131 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2453 net assigned charge : 8.906025 assigned positive charge : 390.7289 centred at (gu) : 84.36676 97.04343 87.63494 assigned negative charge : -381.8235 centred at (gu) : 84.30858 96.24199 88.34997 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 163406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21675 grid for indexing accessible points = 1.400000 m= 81428 mr = 119783 m= 28566 mr = 66648 m= 6433 mr = 23039 m= 770 mr = 4843 m= 27 mr = 456 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3600 time to turn everything in is 1.370000 number of dielectric boundary points 65858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19621 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) : 1.850087 object centre at (A) : 37.42050 27.51650 32.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4195197 6.3509680E-02 midg,1,midg; midg,igrid,midg -0.3648700 -0.2106479 1,midg,midg; igrid,midg,midg -0.1056414 0.1061503 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 23:52:44 rms-change max change #iterations 9.444725 405.6467 at 10iterations 5.426125 142.0431 at 20iterations 3.094394 79.62312 at 30iterations 1.760909 37.79440 at 40iterations 1.000397 19.30154 at 50iterations 0.5705706 13.00217 at 60iterations 0.3248162 6.394623 at 70iterations 0.1846646 3.352459 at 80iterations 0.1049119 1.937553 at 90iterations 5.9659999E-02 1.093166 at 100iterations 3.3892374E-02 0.6357269 at 110iterations 1.9353250E-02 0.4600143 at 120iterations 1.1110926E-02 0.2172699 at 130iterations 6.4174519E-03 0.1232147 at 140iterations 3.7559038E-03 7.5534821E-02 at 150iterations 2.2619863E-03 4.6863556E-02 at 160iterations 1.4207567E-03 3.3348083E-02 at 170iterations 9.4223738E-04 2.4955750E-02 at 180iterations finished qdiffx linear iterations at : 23:52:55 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 9.4223738E-04 2.4955750E-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) 13.07000 DelPhi exited at 23:52:56 13.071u 0.246s 0:13.66 97.4% 0+0k 0+0io 0pf+0w