Sun Oct 9 23:34:52 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+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 Sun Oct 9 2011 at 23:34:52 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 0.6006513 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 0.6006513 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2370 net assigned charge : 1.525008 assigned positive charge : 377.3071 centred at (gu) : 89.18182 90.17894 88.16512 assigned negative charge : -375.7827 centred at (gu) : 89.06743 90.22932 88.14814 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5716 nv = 96 ne = 84 npr = 47913 no. pairs analyzed = 47913 no. exposed pairs = 3090 no. arc points = 21991 no. surface atoms = 1037 nbur = 1396 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 = 1.456000 m= 246 mr = 3010 m= 0 mr = 16 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2700000 number of dielectric boundary points 2936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2235 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4808503E-10 8.8334212E-10 midg,1,midg; midg,igrid,midg 2.4180966E-09 -1.1449164E-09 1,midg,midg; igrid,midg,midg -4.1658383E-09 3.9595593E-09 gauss-seidel spectral radius is 0.9856392 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 23:34:53 rms-change max change #iterations 0.1048483 19.34941 at 10iterations 8.7977787E-03 1.774339 at 20iterations 7.3923974E-04 0.1268072 at 30iterations 6.4076245E-05 9.3803406E-03 at 40iterations 5.5177570E-06 9.8800659E-04 at 50iterations finished qdiffx linear iterations at : 23:34:55 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 5.5177570E-06 9.8800659E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 23:34:56 3.109u 0.148s 0:03.59 90.2% 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 23:34:56 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: SEP 141 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.801954 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 1.801954 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2370 net assigned charge : 1.525008 assigned positive charge : 377.3071 centred at (gu) : 87.54501 90.53622 84.49453 assigned negative charge : -375.7827 centred at (gu) : 87.20206 90.68797 84.44437 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21991 grid for indexing accessible points = 1.400000 m= 20342 mr = 42090 m= 2484 mr = 14598 m= 103 mr = 1421 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1282 time to turn everything in is 0.4500000 number of dielectric boundary points 27261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 18489 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) : 0.6006513 object centre at (A) : 21.92350 -0.5714998 15.79350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5840499E-02 2.6166257E-03 midg,1,midg; midg,igrid,midg -2.4563011E-03 -1.2457551E-03 1,midg,midg; igrid,midg,midg -2.9711142E-02 3.2957792E-02 gauss-seidel spectral radius is 0.9984549 estimated iterations to convergence 202 setup time was (sec) 0.7000000 now iterating at: 23:34:56 rms-change max change #iterations 3.732614 173.8655 at 10iterations 1.656798 71.13669 at 20iterations 0.7403210 26.20680 at 30iterations 0.3296102 12.17339 at 40iterations 0.1468011 5.332560 at 50iterations 6.5248437E-02 2.235638 at 60iterations 2.9192366E-02 1.034161 at 70iterations 1.2981855E-02 0.4646645 at 80iterations 5.7962914E-03 0.2018977 at 90iterations 2.5907224E-03 0.1059723 at 100iterations 1.1520608E-03 4.2787552E-02 at 110iterations 5.1267463E-04 2.1392822E-02 at 120iterations finished qdiffx linear iterations at : 23:35:02 total time elapsed so far: 6.590000 # loops : 120 mean,max change (kT/e) : 5.1267463E-04 2.1392822E-02 energy calculations done at 6.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 23:35:03 6.758u 0.171s 0:07.20 96.1% 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 Sun Oct 9 2011 at 23:35:03 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: SEP 141 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.702931 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): -7.711000 51.55800 ymin,ymax (A): -24.39100 23.24800 zmin,zma (A): -8.941999 40.52900 x,y,z range (A): 59.26900 47.63900 49.47100 scale (grids/A): 2.702931 object centre (A): 21.92350 -0.5714998 15.79350 number of atom coordinates read : 2433 total number of charged atoms : 2370 net assigned charge : 1.525008 assigned positive charge : 377.3071 centred at (gu) : 86.31754 90.80418 81.74176 assigned negative charge : -375.7827 centred at (gu) : 85.80308 91.03191 81.66663 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 144674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21991 grid for indexing accessible points = 1.400000 m= 68201 mr = 102652 m= 21643 mr = 54713 m= 4230 mr = 16959 m= 421 mr = 3046 m= 13 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 4141 time to turn everything in is 1.020000 number of dielectric boundary points 61543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18950 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) : 1.801954 object centre at (A) : 21.92350 -0.5714998 15.79350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2028521 3.1490769E-02 midg,1,midg; midg,igrid,midg -4.5627024E-02 3.2674510E-02 1,midg,midg; igrid,midg,midg -0.5134320 0.4038008 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 1.290000 now iterating at: 23:35:04 rms-change max change #iterations 8.930316 288.7541 at 10iterations 5.079319 125.7439 at 20iterations 2.867985 60.29097 at 30iterations 1.616642 36.14478 at 40iterations 0.9108000 18.88102 at 50iterations 0.5121897 10.68199 at 60iterations 0.2883538 5.540464 at 70iterations 0.1620983 3.284679 at 80iterations 9.1089383E-02 2.000411 at 90iterations 5.1296871E-02 1.140466 at 100iterations 2.8808638E-02 0.5784464 at 110iterations 1.6187387E-02 0.3171921 at 120iterations 9.1182925E-03 0.2037358 at 130iterations 5.1300894E-03 0.1048965 at 140iterations 2.8858862E-03 5.6924820E-02 at 150iterations 1.6277853E-03 3.4202695E-02 at 160iterations 9.1104372E-04 1.8477201E-02 at 170iterations 5.1345961E-04 1.1389256E-02 at 180iterations finished qdiffx linear iterations at : 23:35:13 total time elapsed so far: 10.44000 # loops : 180 mean,max change (kT/e) : 5.1345961E-04 1.1389256E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.63000 DelPhi exited at 23:35:14 10.629u 0.185s 0:11.16 96.7% 0+0k 0+0io 0pf+0w