Tue Oct 11 03:36:33 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 Tue Oct 11 2011 at 03:36:33 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 0.6431914 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 0.6431914 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.499984 assigned positive charge : 326.7234 centred at (gu) : 88.92335 89.57056 90.17068 assigned negative charge : -333.2238 centred at (gu) : 88.75082 89.72733 90.18256 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6268 nv = 96 ne = 84 npr = 45922 no. pairs analyzed = 45922 no. exposed pairs = 2807 no. arc points = 19980 no. surface atoms = 959 nbur = 1268 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3376 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2800000 number of dielectric boundary points 3186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1895 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7412 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5782128E-09 -1.1884385E-08 midg,1,midg; midg,igrid,midg 7.3420257E-09 -2.5163738E-08 1,midg,midg; igrid,midg,midg -3.6985611E-08 6.4728920E-09 gauss-seidel spectral radius is 0.9874467 estimated iterations to convergence 73 setup time was (sec) 0.4900000 now iterating at: 03:36:34 rms-change max change #iterations 0.1357952 23.85654 at 10iterations 1.3921431E-02 2.031052 at 20iterations 1.4069740E-03 0.1929169 at 30iterations 1.3889739E-04 1.8720627E-02 at 40iterations 1.3830402E-05 2.2354126E-03 at 50iterations finished qdiffx linear iterations at : 03:36:36 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.3830402E-05 2.2354126E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 03:36:37 3.090u 0.146s 0:03.62 89.2% 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 Tue Oct 11 2011 at 03:36:37 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 1.929574 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 1.929574 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.499984 assigned positive charge : 326.7234 centred at (gu) : 86.76978 88.71135 90.51192 assigned negative charge : -333.2238 centred at (gu) : 86.25240 89.18180 90.54762 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19980 grid for indexing accessible points = 1.400000 m= 23599 mr = 45536 m= 3809 mr = 17186 m= 222 mr = 2326 m= 6 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 0.4800000 number of dielectric boundary points 29361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 16708 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) : 0.6431914 object centre at (A) : 5.872500 24.04800 22.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6103063E-03 -3.5249233E-02 midg,1,midg; midg,igrid,midg -5.1275477E-02 -6.7083612E-02 1,midg,midg; igrid,midg,midg -1.7984543E-02 1.8510241E-02 gauss-seidel spectral radius is 0.9986350 estimated iterations to convergence 214 setup time was (sec) 0.7400000 now iterating at: 03:36:38 rms-change max change #iterations 3.994119 222.8420 at 10iterations 1.863335 69.73456 at 20iterations 0.8743154 30.58475 at 30iterations 0.4088599 14.21228 at 40iterations 0.1912843 6.130898 at 50iterations 8.9219198E-02 3.118980 at 60iterations 4.1891303E-02 1.450333 at 70iterations 1.9535614E-02 0.6476059 at 80iterations 9.1658561E-03 0.2974143 at 90iterations 4.2786743E-03 0.1556454 at 100iterations 2.0091326E-03 6.9559455E-02 at 110iterations 9.4107847E-04 3.3065796E-02 at 120iterations finished qdiffx linear iterations at : 03:36:44 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 9.4107847E-04 3.3065796E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 03:36:45 6.895u 0.171s 0:07.71 91.5% 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 Tue Oct 11 2011 at 03:36:45 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 2.894361 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): -15.65200 27.39700 ymin,ymax (A): -3.151000 51.24700 zmin,zma (A): -5.250000 50.09900 x,y,z range (A): 43.04900 54.39800 55.34900 scale (grids/A): 2.894361 object centre (A): 5.872500 24.04800 22.42450 number of atom coordinates read : 2227 total number of charged atoms : 2122 net assigned charge : -6.499984 assigned positive charge : 326.7234 centred at (gu) : 85.15460 88.06712 90.76766 assigned negative charge : -333.2238 centred at (gu) : 84.37859 88.77274 90.82148 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19980 grid for indexing accessible points = 1.400000 m= 76038 mr = 110755 m= 28159 mr = 61577 m= 6861 mr = 22436 m= 961 mr = 5018 m= 60 mr = 626 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 548 time to turn everything in is 1.190000 number of dielectric boundary points 66238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16976 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) : 1.929574 object centre at (A) : 5.872500 24.04800 22.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6664760E-02 -0.3297603 midg,1,midg; midg,igrid,midg -0.5120237 -0.9307444 1,midg,midg; igrid,midg,midg -0.1447839 0.2023996 gauss-seidel spectral radius is 0.9992571 estimated iterations to convergence 290 setup time was (sec) 1.460000 now iterating at: 03:36:46 rms-change max change #iterations 9.232392 346.1496 at 10iterations 5.343875 124.4692 at 20iterations 3.076643 62.25900 at 30iterations 1.768011 35.04744 at 40iterations 1.014845 19.96210 at 50iterations 0.5826644 12.94783 at 60iterations 0.3345109 6.108536 at 70iterations 0.1917605 3.885192 at 80iterations 0.1099921 1.982628 at 90iterations 6.2882841E-02 1.346992 at 100iterations 3.5987146E-02 0.6350260 at 110iterations 2.0676984E-02 0.3837433 at 120iterations 1.1839894E-02 0.2450600 at 130iterations 6.7724106E-03 0.1433697 at 140iterations 3.8756884E-03 7.9823017E-02 at 150iterations 2.2199994E-03 4.1962624E-02 at 160iterations 1.2690932E-03 2.3983479E-02 at 170iterations 7.2903960E-04 1.5480518E-02 at 180iterations finished qdiffx linear iterations at : 03:36:56 total time elapsed so far: 10.91000 # loops : 180 mean,max change (kT/e) : 7.2903960E-04 1.5480518E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 03:36:56 11.090u 0.173s 0:11.79 95.5% 0+0k 0+0io 0pf+0w