Sun Oct 9 15:59:45 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 15:59:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3060 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: 0.6361687 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): -15.08000 37.02600 ymin,ymax (A): 3.470000 56.46500 zmin,zma (A): -34.42700 21.53300 x,y,z range (A): 52.10600 52.99500 55.96000 scale (grids/A): 0.6361687 object centre (A): 10.97300 29.96750 -6.447000 number of atom coordinates read : 3060 total number of charged atoms : 2916 net assigned charge : -4.499987 assigned positive charge : 451.3192 centred at (gu) : 90.41158 91.17378 88.68238 assigned negative charge : -455.8206 centred at (gu) : 90.45776 91.28532 88.62615 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8291 nv = 96 ne = 84 npr = 63136 no. pairs analyzed = 63136 no. exposed pairs = 3777 no. arc points = 26648 no. surface atoms = 1275 nbur = 1785 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4589 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6579687E-08 9.3909314E-10 midg,1,midg; midg,igrid,midg 6.1437340E-09 -2.5044498E-08 1,midg,midg; igrid,midg,midg 8.2873486E-11 -1.2261123E-08 gauss-seidel spectral radius is 0.9872406 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 15:59:46 rms-change max change #iterations 0.1557120 22.77221 at 10iterations 1.5267036E-02 2.098621 at 20iterations 1.5567620E-03 0.2217889 at 30iterations 2.4745855E-04 3.9014816E-02 at 40iterations 7.9260048E-05 1.5349388E-02 at 50iterations finished qdiffx linear iterations at : 15:59:49 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 7.9260048E-05 1.5349388E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 15:59:50 3.577u 0.413s 0:04.30 92.5% 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 15:59:50 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 = 3060 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: 1.908506 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): -15.08000 37.02600 ymin,ymax (A): 3.470000 56.46500 zmin,zma (A): -34.42700 21.53300 x,y,z range (A): 52.10600 52.99500 55.96000 scale (grids/A): 1.908506 object centre (A): 10.97300 29.96750 -6.447000 number of atom coordinates read : 3060 total number of charged atoms : 2916 net assigned charge : -4.499987 assigned positive charge : 451.3192 centred at (gu) : 91.23403 93.52067 86.04620 assigned negative charge : -455.8206 centred at (gu) : 91.37294 93.85571 85.87830 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26648 grid for indexing accessible points = 1.400000 m= 32540 mr = 62757 m= 5457 mr = 23695 m= 302 mr = 3425 m= 3 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 38161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 22953 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) : 0.6361687 object centre at (A) : 10.97300 29.96750 -6.447000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5396722E-03 2.6988124E-02 midg,1,midg; midg,igrid,midg -2.2386907E-02 -4.0390406E-02 1,midg,midg; igrid,midg,midg -1.3643031E-02 -3.4764651E-02 gauss-seidel spectral radius is 0.9986827 estimated iterations to convergence 218 setup time was (sec) 0.6600000 now iterating at: 15:59:50 rms-change max change #iterations 4.638724 200.6715 at 10iterations 2.204893 72.56560 at 20iterations 1.041494 32.09792 at 30iterations 0.4941011 15.02248 at 40iterations 0.2338563 7.323542 at 50iterations 0.1114445 3.201675 at 60iterations 5.2962702E-02 1.475689 at 70iterations 2.5136508E-02 0.7603083 at 80iterations 1.1954921E-02 0.3624325 at 90iterations 5.6717056E-03 0.1680575 at 100iterations 2.7158028E-03 7.9543114E-02 at 110iterations 1.3027299E-03 3.7076950E-02 at 120iterations finished qdiffx linear iterations at : 15:59:58 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 1.3027299E-03 3.7076950E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 15:59:59 8.162u 0.816s 0:09.31 96.3% 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 15:59:59 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 = 3060 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: 2.862759 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): -15.08000 37.02600 ymin,ymax (A): 3.470000 56.46500 zmin,zma (A): -34.42700 21.53300 x,y,z range (A): 52.10600 52.99500 55.96000 scale (grids/A): 2.862759 object centre (A): 10.97300 29.96750 -6.447000 number of atom coordinates read : 3060 total number of charged atoms : 2916 net assigned charge : -4.499987 assigned positive charge : 451.3192 centred at (gu) : 91.85077 95.28086 84.06911 assigned negative charge : -455.8206 centred at (gu) : 92.05956 95.78345 83.81751 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 208134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26648 grid for indexing accessible points = 1.400000 m= 104297 mr = 152448 m= 38717 mr = 84844 m= 9827 mr = 30747 m= 1387 mr = 7270 m= 68 mr = 930 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 86174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 23325 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) : 1.908506 object centre at (A) : 10.97300 29.96750 -6.447000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2070692 0.7107195 midg,1,midg; midg,igrid,midg -0.3610886 -0.4123685 1,midg,midg; igrid,midg,midg -0.2312800 -0.3481882 gauss-seidel spectral radius is 0.9992831 estimated iterations to convergence 295 setup time was (sec) 1.430000 now iterating at: 16:00:01 rms-change max change #iterations 10.96406 436.6425 at 10iterations 6.506836 149.8906 at 20iterations 3.832906 75.77106 at 30iterations 2.251163 49.99467 at 40iterations 1.317654 29.88640 at 50iterations 0.7710837 15.16445 at 60iterations 0.4500316 8.253716 at 70iterations 0.2626923 6.058546 at 80iterations 0.1528872 2.814152 at 90iterations 8.8877380E-02 1.558456 at 100iterations 5.1709618E-02 1.048943 at 110iterations 3.0077940E-02 0.5752354 at 120iterations 1.7476358E-02 0.3461325 at 130iterations 1.0159410E-02 0.1995378 at 140iterations 5.8968323E-03 0.1104317 at 150iterations 3.4491175E-03 6.4692974E-02 at 160iterations 2.0147753E-03 3.9999008E-02 at 170iterations 1.1919745E-03 2.1570206E-02 at 180iterations finished qdiffx linear iterations at : 16:00:15 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 1.1919745E-03 2.1570206E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.84000 DelPhi exited at 16:00:16 14.841u 1.454s 0:16.58 98.2% 0+0k 0+0io 0pf+0w