Sat Oct 15 11:29:20 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 11:29:20 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 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: 0.5822987 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 0.5822987 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 479.3998 centred at (gu) : 88.36047 89.67607 91.48592 assigned negative charge : -473.4010 centred at (gu) : 88.27206 89.81863 91.50364 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7423 nv = 96 ne = 84 npr = 62736 no. pairs analyzed = 62736 no. exposed pairs = 4351 no. arc points = 30794 no. surface atoms = 1443 nbur = 1753 mkacc time = 9.9999994E-02 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 = 1.484000 m= 374 mr = 3800 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3018 ## 303 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3531740E-09 1.3990559E-09 midg,1,midg; midg,igrid,midg 5.3678724E-09 -2.0272835E-09 1,midg,midg; igrid,midg,midg -1.2207139E-09 2.5012679E-09 gauss-seidel spectral radius is 0.9848064 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 11:29:21 rms-change max change #iterations 0.1059443 15.56222 at 10iterations 9.2728203E-03 1.791817 at 20iterations 1.3678485E-03 0.1965752 at 30iterations 3.7483621E-04 5.9619904E-02 at 40iterations 1.1410250E-04 1.7948151E-02 at 50iterations finished qdiffx linear iterations at : 11:29:26 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.1410250E-04 1.7948151E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 11:29:26 3.666u 0.212s 0:06.20 62.4% 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 11:29:26 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 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: 1.746896 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 1.746896 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 479.3998 centred at (gu) : 85.08067 89.02744 94.45714 assigned negative charge : -473.4010 centred at (gu) : 84.81607 89.45553 94.51081 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30794 grid for indexing accessible points = 1.400000 m= 28005 mr = 54394 m= 3802 mr = 19400 m= 158 mr = 2127 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.4000000 number of dielectric boundary points 37067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23785 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) : 0.5822987 object centre at (A) : 81.33050 11.21100 -5.144502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6833561E-02 2.4639182E-02 midg,1,midg; midg,igrid,midg 2.0650009E-02 -1.3317356E-02 1,midg,midg; igrid,midg,midg -2.5752541E-03 5.7041966E-03 gauss-seidel spectral radius is 0.9984542 estimated iterations to convergence 202 setup time was (sec) 0.6400000 now iterating at: 11:29:27 rms-change max change #iterations 4.040576 171.9053 at 10iterations 1.783020 70.28714 at 20iterations 0.7951409 28.00799 at 30iterations 0.3547105 11.95014 at 40iterations 0.1581930 6.350266 at 50iterations 7.0603035E-02 2.172977 at 60iterations 3.1678010E-02 1.039352 at 70iterations 1.4278821E-02 0.4552422 at 80iterations 6.5657324E-03 0.2066498 at 90iterations 3.1142696E-03 0.1222878 at 100iterations 1.5364437E-03 5.7502747E-02 at 110iterations 8.1923680E-04 2.8374672E-02 at 120iterations finished qdiffx linear iterations at : 11:29:40 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 8.1923680E-04 2.8374672E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 11:29:41 8.267u 0.237s 0:14.78 57.4% 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 11:29:42 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3196 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: 2.620344 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 2.620344 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 479.3998 centred at (gu) : 82.62094 88.54076 96.68536 assigned negative charge : -473.4010 centred at (gu) : 82.22400 89.18320 96.76612 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30794 grid for indexing accessible points = 1.400000 m= 92003 mr = 133072 m= 30941 mr = 72641 m= 6305 mr = 23689 m= 541 mr = 4335 m= 14 mr = 231 m= 0 mr = 4 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 1.050000 number of dielectric boundary points 83502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 24432 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) : 1.746896 object centre at (A) : 81.33050 11.21100 -5.144502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1797609 0.1962835 midg,1,midg; midg,igrid,midg 0.2823008 -0.1949042 1,midg,midg; igrid,midg,midg 0.3847995 1.8258498E-03 gauss-seidel spectral radius is 0.9992269 estimated iterations to convergence 284 setup time was (sec) 1.330000 now iterating at: 11:29:44 rms-change max change #iterations 10.18145 287.3060 at 10iterations 6.019217 167.1448 at 20iterations 3.518679 84.66388 at 30iterations 2.043376 51.06140 at 40iterations 1.181519 30.87893 at 50iterations 0.6809196 14.03051 at 60iterations 0.3920232 7.968143 at 70iterations 0.2245202 4.554596 at 80iterations 0.1285883 2.467207 at 90iterations 7.3541068E-02 1.469212 at 100iterations 4.1994046E-02 0.8732872 at 110iterations 2.3964714E-02 0.4953156 at 120iterations 1.3687975E-02 0.2766647 at 130iterations 7.8406846E-03 0.1526108 at 140iterations 4.4862423E-03 8.1302643E-02 at 150iterations 2.5862951E-03 4.8347473E-02 at 160iterations 1.5091773E-03 3.0757904E-02 at 170iterations 8.9603727E-04 1.9531250E-02 at 180iterations finished qdiffx linear iterations at : 11:30:01 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 8.9603727E-04 1.9531250E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 11:30:01 14.019u 0.271s 0:19.37 73.7% 0+0k 0+0io 0pf+0w