Sat Oct 8 15:56:34 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 8 2011 at 15:56:34 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 = 2358 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: 0.5834248 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 0.5834248 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2269 net assigned charge : 3.000001 assigned positive charge : 349.1231 centred at (gu) : 90.53356 88.60016 88.91196 assigned negative charge : -346.1237 centred at (gu) : 90.54703 88.74402 88.96426 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5189 nv = 96 ne = 84 npr = 48464 no. pairs analyzed = 48464 no. exposed pairs = 2914 no. arc points = 20314 no. surface atoms = 1000 nbur = 1358 mkacc time = 0.1300000 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= 222 mr = 2754 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3300000 number of dielectric boundary points 2647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2096 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1639923E-09 -2.4289193E-10 midg,1,midg; midg,igrid,midg 4.7204325E-09 -1.5134803E-09 1,midg,midg; igrid,midg,midg 8.3351676E-10 4.7804516E-10 gauss-seidel spectral radius is 0.9847810 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 15:56:35 rms-change max change #iterations 8.7948702E-02 16.23266 at 10iterations 6.9515873E-03 1.168179 at 20iterations 5.9218088E-04 9.6633911E-02 at 30iterations 7.0222617E-05 1.0883391E-02 at 40iterations 1.3461920E-05 2.3429394E-03 at 50iterations finished qdiffx linear iterations at : 15:56:38 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 1.3461920E-05 2.3429394E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 15:56:39 4.046u 0.269s 0:04.62 93.0% 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 Sat Oct 8 2011 at 15:56:39 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 = 2358 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: 1.750274 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 1.750274 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2269 net assigned charge : 3.000001 assigned positive charge : 349.1231 centred at (gu) : 91.60030 85.80006 86.73544 assigned negative charge : -346.1237 centred at (gu) : 91.64091 86.23184 86.89263 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20314 grid for indexing accessible points = 1.400000 m= 18236 mr = 39267 m= 2226 mr = 12883 m= 71 mr = 1297 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1057 time to turn everything in is 0.5300000 number of dielectric boundary points 24455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17670 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) : 0.5834248 object centre at (A) : 21.65200 7.344501 11.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5682306E-02 1.1394885E-02 midg,1,midg; midg,igrid,midg 1.4283173E-02 -3.2703304E-03 1,midg,midg; igrid,midg,midg 2.0607959E-03 -1.5873892E-02 gauss-seidel spectral radius is 0.9983563 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 15:56:40 rms-change max change #iterations 3.333233 183.8691 at 10iterations 1.452977 56.29285 at 20iterations 0.6346369 22.28999 at 30iterations 0.2761711 10.69956 at 40iterations 0.1209642 4.534265 at 50iterations 5.2461132E-02 1.819777 at 60iterations 2.2904145E-02 0.8670158 at 70iterations 9.9889450E-03 0.3976407 at 80iterations 4.3508979E-03 0.1512966 at 90iterations 1.9035971E-03 6.7773819E-02 at 100iterations 8.2856446E-04 3.1338692E-02 at 110iterations 3.6366441E-04 1.4320374E-02 at 120iterations finished qdiffx linear iterations at : 15:56:48 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 3.6366441E-04 1.4320374E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 15:56:49 9.135u 0.280s 0:09.74 96.6% 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 8 2011 at 15:56:49 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 = 2358 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: 2.625412 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 2.625412 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2269 net assigned charge : 3.000001 assigned positive charge : 349.1231 centred at (gu) : 92.40046 83.69993 85.10300 assigned negative charge : -346.1237 centred at (gu) : 92.46131 84.34771 85.33891 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 133155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20314 grid for indexing accessible points = 1.400000 m= 61643 mr = 95841 m= 19384 mr = 49172 m= 3847 mr = 15217 m= 328 mr = 2776 m= 12 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3583 time to turn everything in is 1.280000 number of dielectric boundary points 55168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18149 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) : 1.750274 object centre at (A) : 21.65200 7.344501 11.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2109814 0.3799198 midg,1,midg; midg,igrid,midg 0.1599924 -4.7754928E-02 1,midg,midg; igrid,midg,midg 4.1271959E-02 -0.2688862 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 1.610000 now iterating at: 15:56:50 rms-change max change #iterations 8.284617 286.1385 at 10iterations 4.718343 112.0763 at 20iterations 2.662613 63.13111 at 30iterations 1.500054 45.37674 at 40iterations 0.8443485 17.98951 at 50iterations 0.4753222 10.53709 at 60iterations 0.2659010 6.372021 at 70iterations 0.1487330 3.261885 at 80iterations 8.3101355E-02 1.769901 at 90iterations 4.6421919E-02 1.042793 at 100iterations 2.5932644E-02 0.5750885 at 110iterations 1.4497225E-02 0.2820535 at 120iterations 8.0910213E-03 0.1708665 at 130iterations 4.5078387E-03 9.0332031E-02 at 140iterations 2.5141779E-03 5.1567078E-02 at 150iterations 1.4021863E-03 2.9655695E-02 at 160iterations 7.8331021E-04 1.7191887E-02 at 170iterations 4.3822810E-04 9.7122192E-03 at 180iterations finished qdiffx linear iterations at : 15:57:04 total time elapsed so far: 14.69000 # loops : 180 mean,max change (kT/e) : 4.3822810E-04 9.7122192E-03 energy calculations done at 14.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.87000 DelPhi exited at 15:57:04 14.869u 0.278s 0:15.51 97.5% 0+0k 0+0io 0pf+0w