Sat Oct 15 12:15:52 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 12:15:52 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 = 3190 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: 0.5485023 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 0.5485023 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.000040 assigned positive charge : 469.5079 centred at (gu) : 90.29652 88.54716 90.63570 assigned negative charge : -462.5093 centred at (gu) : 90.31251 88.48344 90.55056 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6418 nv = 96 ne = 84 npr = 62995 no. pairs analyzed = 62995 no. exposed pairs = 4202 no. arc points = 29346 no. surface atoms = 1413 nbur = 1777 mkacc time = 0.1100000 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 = 1.540000 m= 262 mr = 3281 m= 0 mr = 4 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 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8295 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4034422E-10 1.3120864E-09 midg,1,midg; midg,igrid,midg -1.6069137E-11 6.7640149E-10 1,midg,midg; igrid,midg,midg 5.6279387E-10 3.8859824E-10 gauss-seidel spectral radius is 0.9828833 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 12:15:53 rms-change max change #iterations 7.7482902E-02 12.47411 at 10iterations 5.0886287E-03 0.9078827 at 20iterations 3.4935703E-04 6.1508179E-02 at 30iterations 2.6237547E-05 3.7055016E-03 at 40iterations 3.1509917E-06 5.3751469E-04 at 50iterations finished qdiffx linear iterations at : 12:15:56 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 3.1509917E-06 5.3751469E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 12:15:56 3.645u 0.220s 0:04.13 93.4% 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 Sat Oct 15 2011 at 12:15:56 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 = 3190 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: 1.645507 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 1.645507 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.000040 assigned positive charge : 469.5079 centred at (gu) : 90.88856 85.64061 91.90620 assigned negative charge : -462.5093 centred at (gu) : 90.93743 85.44991 91.65126 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22308 mr = 47975 m= 2409 mr = 15019 m= 62 mr = 1063 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.3600000 number of dielectric boundary points 31562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 312 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 23403 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) : 0.5485023 object centre at (A) : 6.376499 86.45000 26.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4279418E-03 2.5925369E-03 midg,1,midg; midg,igrid,midg 1.0434993E-02 1.7993217E-02 1,midg,midg; igrid,midg,midg 2.2957765E-02 7.3564111E-04 gauss-seidel spectral radius is 0.9982430 estimated iterations to convergence 189 setup time was (sec) 0.6100000 now iterating at: 12:15:57 rms-change max change #iterations 3.451266 154.4787 at 10iterations 1.456045 59.82339 at 20iterations 0.6150775 22.04455 at 30iterations 0.2595173 8.789763 at 40iterations 0.1091995 3.809150 at 50iterations 4.6150006E-02 1.452629 at 60iterations 1.9522205E-02 0.6659641 at 70iterations 8.2666343E-03 0.2882390 at 80iterations 3.5092379E-03 0.1262360 at 90iterations 1.4821532E-03 5.4712296E-02 at 100iterations 6.2712358E-04 2.1097183E-02 at 110iterations 2.6727436E-04 9.3460083E-03 at 120iterations finished qdiffx linear iterations at : 12:16:05 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 2.6727436E-04 9.3460083E-03 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 12:16:05 8.376u 0.226s 0:09.03 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 12:16:05 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 = 3190 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: 2.468261 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 2.468261 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.000040 assigned positive charge : 469.5079 centred at (gu) : 91.33276 83.46080 92.85912 assigned negative charge : -462.5093 centred at (gu) : 91.40599 83.17470 92.47691 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29346 grid for indexing accessible points = 1.400000 m= 76637 mr = 117695 m= 22353 mr = 59720 m= 3597 mr = 16405 m= 225 mr = 2186 m= 6 mr = 80 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1030 time to turn everything in is 0.9000000 number of dielectric boundary points 71336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 24333 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) : 1.645507 object centre at (A) : 6.376499 86.45000 26.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1177633 2.3763893E-02 midg,1,midg; midg,igrid,midg 0.1643693 0.3797188 1,midg,midg; igrid,midg,midg 0.4536198 -1.9113753E-02 gauss-seidel spectral radius is 0.9991632 estimated iterations to convergence 273 setup time was (sec) 1.150000 now iterating at: 12:16:07 rms-change max change #iterations 8.962774 348.3480 at 10iterations 5.115340 148.5205 at 20iterations 2.883972 76.87288 at 30iterations 1.624490 42.68212 at 40iterations 0.9087898 20.24887 at 50iterations 0.5088717 10.47067 at 60iterations 0.2834130 6.201829 at 70iterations 0.1586283 3.180395 at 80iterations 8.7979145E-02 1.856655 at 90iterations 4.8951406E-02 1.007656 at 100iterations 2.7237244E-02 0.5659447 at 110iterations 1.5131300E-02 0.3246317 at 120iterations 8.3861910E-03 0.1824036 at 130iterations 4.6565072E-03 9.3169212E-02 at 140iterations 2.5810411E-03 5.1057816E-02 at 150iterations 1.4328187E-03 2.9982090E-02 at 160iterations 7.9597248E-04 1.6416550E-02 at 170iterations 4.4189632E-04 9.2816353E-03 at 180iterations finished qdiffx linear iterations at : 12:16:19 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 4.4189632E-04 9.2816353E-03 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 12:16:20 13.590u 0.269s 0:14.15 97.8% 0+0k 0+0io 0pf+0w