Sun Oct 9 16:29:01 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 16:29:01 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 = 2402 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: 0.6257030 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): 22.62400 79.52000 ymin,ymax (A): 11.81900 67.41100 zmin,zma (A): 2.354000 49.57800 x,y,z range (A): 56.89600 55.59200 47.22400 scale (grids/A): 0.6257030 object centre (A): 51.07200 39.61500 25.96600 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 7.7933073E-06 assigned positive charge : 365.9232 centred at (gu) : 87.63490 89.04104 89.16347 assigned negative charge : -365.9236 centred at (gu) : 87.50719 88.96258 89.35029 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6327 nv = 96 ne = 84 npr = 48211 no. pairs analyzed = 48211 no. exposed pairs = 3174 no. arc points = 22010 no. surface atoms = 1070 nbur = 1332 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 308 mr = 3286 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1700000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7717 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6395949E-08 -1.1428027E-08 midg,1,midg; midg,igrid,midg -6.9284445E-09 4.7703570E-09 1,midg,midg; igrid,midg,midg -1.5840742E-08 5.6079279E-09 gauss-seidel spectral radius is 0.9867574 estimated iterations to convergence 71 setup time was (sec) 0.3500000 now iterating at: 16:29:02 rms-change max change #iterations 0.1236832 18.28301 at 10iterations 1.1481743E-02 1.763000 at 20iterations 1.0987902E-03 0.1639595 at 30iterations 1.1885133E-04 2.7523994E-02 at 40iterations 2.6472015E-05 5.6509972E-03 at 50iterations finished qdiffx linear iterations at : 16:29:05 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.6472015E-05 5.6509972E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:29:05 3.391u 0.212s 0:03.91 92.0% 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 16:29:05 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 = 2402 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: 1.877109 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): 22.62400 79.52000 ymin,ymax (A): 11.81900 67.41100 zmin,zma (A): 2.354000 49.57800 x,y,z range (A): 56.89600 55.59200 47.22400 scale (grids/A): 1.877109 object centre (A): 51.07200 39.61500 25.96600 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 7.7933073E-06 assigned positive charge : 365.9232 centred at (gu) : 82.90434 87.12255 87.49007 assigned negative charge : -365.9236 centred at (gu) : 82.52148 86.88763 88.05070 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22010 grid for indexing accessible points = 1.400000 m= 22778 mr = 46443 m= 3010 mr = 15770 m= 161 mr = 1554 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 0.3600000 number of dielectric boundary points 31032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17771 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) : 0.6257030 object centre at (A) : 51.07200 39.61500 25.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3020679E-02 -1.5960496E-02 midg,1,midg; midg,igrid,midg 8.2649421E-03 4.0040854E-02 1,midg,midg; igrid,midg,midg -4.6659369E-02 4.1253175E-04 gauss-seidel spectral radius is 0.9985713 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 16:29:06 rms-change max change #iterations 3.990722 182.2915 at 10iterations 1.826077 70.29504 at 20iterations 0.8395118 28.19538 at 30iterations 0.3851056 13.03680 at 40iterations 0.1776352 5.988289 at 50iterations 8.1361488E-02 2.647507 at 60iterations 3.7456062E-02 1.183568 at 70iterations 1.7177356E-02 0.5633497 at 80iterations 7.8968918E-03 0.2528372 at 90iterations 3.6349746E-03 0.1231346 at 100iterations 1.6647027E-03 5.6730270E-02 at 110iterations 7.6937844E-04 2.7379990E-02 at 120iterations finished qdiffx linear iterations at : 16:29:13 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 7.6937844E-04 2.7379990E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 16:29:14 7.882u 0.194s 0:08.36 96.5% 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 16:29:14 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 = 2402 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: 2.815664 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): 22.62400 79.52000 ymin,ymax (A): 11.81900 67.41100 zmin,zma (A): 2.354000 49.57800 x,y,z range (A): 56.89600 55.59200 47.22400 scale (grids/A): 2.815664 object centre (A): 51.07200 39.61500 25.96600 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 7.7933073E-06 assigned positive charge : 365.9232 centred at (gu) : 79.35632 85.68388 86.23502 assigned negative charge : -365.9236 centred at (gu) : 78.78215 85.33142 87.07602 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 159531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22010 grid for indexing accessible points = 1.400000 m= 76330 mr = 113391 m= 24261 mr = 60567 m= 4852 mr = 18164 m= 696 mr = 3297 m= 42 mr = 396 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2584 time to turn everything in is 0.8700000 number of dielectric boundary points 69890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 18115 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) : 1.877109 object centre at (A) : 51.07200 39.61500 25.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1860147 -0.1492654 midg,1,midg; midg,igrid,midg 0.1522094 0.5370256 1,midg,midg; igrid,midg,midg -0.4116747 -0.1191207 gauss-seidel spectral radius is 0.9992475 estimated iterations to convergence 288 setup time was (sec) 1.110000 now iterating at: 16:29:15 rms-change max change #iterations 9.570759 346.4417 at 10iterations 5.594594 129.8504 at 20iterations 3.243368 72.77921 at 30iterations 1.874360 42.16299 at 40iterations 1.079392 28.23007 at 50iterations 0.6207194 13.06996 at 60iterations 0.3564042 8.310269 at 70iterations 0.2043702 4.146865 at 80iterations 0.1170779 2.391940 at 90iterations 6.7171268E-02 1.366125 at 100iterations 3.8480084E-02 0.8402328 at 110iterations 2.1992905E-02 0.4280853 at 120iterations 1.2611995E-02 0.2556763 at 130iterations 7.2078602E-03 0.1431521 at 140iterations 4.1188477E-03 7.7377319E-02 at 150iterations 2.3597092E-03 4.7128677E-02 at 160iterations 1.3459183E-03 2.7120590E-02 at 170iterations 7.6969626E-04 1.4929771E-02 at 180iterations finished qdiffx linear iterations at : 16:29:26 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 7.6969626E-04 1.4929771E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 16:29:27 12.554u 0.202s 0:13.03 97.8% 0+0k 0+0io 0pf+0w