Sun Oct 9 08:26:15 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 08:26:15 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 = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4820060 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 0.4820060 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.21267 89.73979 89.16846 assigned negative charge : -884.0535 centred at (gu) : 90.33367 89.72366 89.13573 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8507 nv = 96 ne = 84 npr = 117632 no. pairs analyzed = 117632 no. exposed pairs = 7387 no. arc points = 51578 no. surface atoms = 2475 nbur = 3393 mkacc time = 0.2500000 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 = 1.764000 m= 289 mr = 4320 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4854 ## 840 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8902348E-11 8.4781409E-12 midg,1,midg; midg,igrid,midg -3.4374191E-11 -3.4197018E-12 1,midg,midg; igrid,midg,midg 8.1762770E-11 -1.3380529E-10 gauss-seidel spectral radius is 0.9780820 estimated iterations to convergence 56 setup time was (sec) 0.7600000 now iterating at: 08:26:16 rms-change max change #iterations 5.5420540E-02 7.777756 at 10iterations 3.2133418E-03 0.6869202 at 20iterations 5.0561543E-04 0.1268692 at 30iterations 1.3991488E-04 3.3866882E-02 at 40iterations 4.2132437E-05 9.4909668E-03 at 50iterations finished qdiffx linear iterations at : 08:26:19 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.2132437E-05 9.4909668E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:26:19 3.423u 0.159s 0:03.85 92.7% 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 08:26:19 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 = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.446018 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 1.446018 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.63618 89.21745 87.50360 assigned negative charge : -884.0535 centred at (gu) : 91.00068 89.17065 87.40661 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 97685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26530 mr = 66492 m= 1845 mr = 17105 m= 26 mr = 671 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1338 time to turn everything in is 0.6600000 number of dielectric boundary points 41818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 830 ## 25 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 41895 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) : 0.4820060 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1230064E-02 -3.9445795E-03 midg,1,midg; midg,igrid,midg 6.8550115E-04 1.9635791E-03 1,midg,midg; igrid,midg,midg 5.5028205E-03 -1.1778692E-02 gauss-seidel spectral radius is 0.9979612 estimated iterations to convergence 176 setup time was (sec) 0.9300000 now iterating at: 08:26:20 rms-change max change #iterations 3.734089 144.2236 at 10iterations 1.476211 52.86272 at 20iterations 0.5850341 19.15650 at 30iterations 0.2320549 7.201379 at 40iterations 9.2040256E-02 2.969249 at 50iterations 3.6664478E-02 1.280548 at 60iterations 1.4592811E-02 0.4954448 at 70iterations 5.8560409E-03 0.2009392 at 80iterations 2.3804414E-03 7.6099455E-02 at 90iterations 1.0001693E-03 3.7948608E-02 at 100iterations 4.4759925E-04 1.7974854E-02 at 110iterations 2.2000416E-04 8.6984634E-03 at 120iterations finished qdiffx linear iterations at : 08:26:26 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.2000416E-04 8.6984634E-03 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 08:26:27 7.325u 0.189s 0:07.80 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 08:26:27 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 = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2500000 grid size : 179 scale,in grids/A, set to be: 2.169027 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 2.169027 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.95393 88.82581 86.25498 assigned negative charge : -884.0535 centred at (gu) : 91.50108 88.75593 86.10999 start vw surface at 0.3600000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 228238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 98246 mr = 164389 m= 21981 mr = 75410 m= 2446 mr = 15294 m= 71 mr = 1341 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 4426 time to turn everything in is 1.800000 number of dielectric boundary points 94544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 45349 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) : 1.446018 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2375945 -0.1185339 midg,1,midg; midg,igrid,midg 4.3300420E-02 4.7040626E-02 1,midg,midg; igrid,midg,midg 0.1939106 -0.1811043 gauss-seidel spectral radius is 0.9991482 estimated iterations to convergence 271 setup time was (sec) 2.120000 now iterating at: 08:26:29 rms-change max change #iterations 10.58867 278.7939 at 10iterations 6.052322 143.7319 at 20iterations 3.446320 89.49408 at 30iterations 1.955005 41.29097 at 40iterations 1.100677 23.96379 at 50iterations 0.6203943 14.34789 at 60iterations 0.3479085 6.910854 at 70iterations 0.1942363 3.688662 at 80iterations 0.1086930 2.252423 at 90iterations 6.0619302E-02 1.254811 at 100iterations 3.3757742E-02 0.6618557 at 110iterations 1.8825356E-02 0.3572083 at 120iterations 1.0469615E-02 0.1999941 at 130iterations 5.8373301E-03 0.1017570 at 140iterations 3.2576073E-03 6.2185764E-02 at 150iterations 1.8208806E-03 3.0990601E-02 at 160iterations 1.0224094E-03 1.8173218E-02 at 170iterations 5.8007723E-04 1.0189056E-02 at 180iterations finished qdiffx linear iterations at : 08:26:40 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 5.8007723E-04 1.0189056E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 08:26:41 13.006u 0.196s 0:13.48 97.8% 0+0k 0+0io 0pf+0w