Sun Oct 9 07:56:01 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 07:56:01 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 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: 0.7062371 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 0.7062371 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 334.2635 centred at (gu) : 90.03682 90.76936 90.78271 assigned negative charge : -328.2639 centred at (gu) : 89.93053 90.85346 90.91218 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7407 nv = 96 ne = 84 npr = 45763 no. pairs analyzed = 45763 no. exposed pairs = 2774 no. arc points = 19871 no. surface atoms = 938 nbur = 1273 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4050 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.2700000 number of dielectric boundary points 3732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1842 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8655420E-08 -1.9482000E-08 midg,1,midg; midg,igrid,midg 7.9633267E-08 7.9511544E-09 1,midg,midg; igrid,midg,midg -4.1152179E-09 1.0411544E-07 gauss-seidel spectral radius is 0.9895663 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 07:56:02 rms-change max change #iterations 0.2038693 30.47168 at 10iterations 2.5390109E-02 3.694855 at 20iterations 3.1024187E-03 0.4399917 at 30iterations 3.8304145E-04 6.5433025E-02 at 40iterations 4.6902333E-05 5.9318542E-03 at 50iterations finished qdiffx linear iterations at : 07:56:05 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.6902333E-05 5.9318542E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 07:56:05 3.509u 0.244s 0:04.03 92.8% 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 07:56:05 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 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: 2.118711 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 2.118711 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 334.2635 centred at (gu) : 90.11002 92.30771 92.34787 assigned negative charge : -328.2639 centred at (gu) : 89.79128 92.56028 92.73641 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19871 grid for indexing accessible points = 1.400000 m= 30466 mr = 53926 m= 5985 mr = 22722 m= 578 mr = 3938 m= 24 mr = 287 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1717 time to turn everything in is 0.5900000 number of dielectric boundary points 34474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16464 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) : 0.7062371 object centre at (A) : 7.084000 1.0004044E-03 15.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8316773E-02 1.1982743E-02 midg,1,midg; midg,igrid,midg 3.5762712E-02 2.4701701E-02 1,midg,midg; igrid,midg,midg -1.3370670E-02 3.3185374E-02 gauss-seidel spectral radius is 0.9988450 estimated iterations to convergence 233 setup time was (sec) 0.9000000 now iterating at: 07:56:07 rms-change max change #iterations 4.870022 244.0473 at 10iterations 2.405038 76.07996 at 20iterations 1.196775 35.93537 at 30iterations 0.5951917 17.61082 at 40iterations 0.2958333 8.709870 at 50iterations 0.1470796 4.473532 at 60iterations 7.3294789E-02 2.385022 at 70iterations 3.6448687E-02 1.020878 at 80iterations 1.8186178E-02 0.5012207 at 90iterations 9.0072788E-03 0.2805595 at 100iterations 4.4963164E-03 0.1236286 at 110iterations 2.2310663E-03 6.3581467E-02 at 120iterations finished qdiffx linear iterations at : 07:56:14 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 2.2310663E-03 6.3581467E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 07:56:14 8.505u 0.264s 0:09.04 96.9% 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 07:56:15 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 208 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: 3.178067 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): -16.39100 30.55900 ymin,ymax (A): -25.20300 25.20500 zmin,zma (A): -4.444000 34.59400 x,y,z range (A): 46.95000 50.40800 39.03800 scale (grids/A): 3.178067 object centre (A): 7.084000 1.0004044E-03 15.07500 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 334.2635 centred at (gu) : 90.16506 93.46152 93.52186 assigned negative charge : -328.2639 centred at (gu) : 89.68692 93.84026 94.10471 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 180306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19871 grid for indexing accessible points = 1.400000 m= 94558 mr = 129962 m= 38778 mr = 77660 m= 11385 mr = 31716 m= 2328 mr = 8703 m= 293 mr = 1648 m= 13 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 5717 time to turn everything in is 1.830000 number of dielectric boundary points 77807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 16592 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) : 2.118711 object centre at (A) : 7.084000 1.0004044E-03 15.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6267287 0.1307908 midg,1,midg; midg,igrid,midg 0.2359114 0.3690856 1,midg,midg; igrid,midg,midg -6.3988857E-02 0.2128330 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 298 setup time was (sec) 2.160000 now iterating at: 07:56:17 rms-change max change #iterations 10.63982 423.8386 at 10iterations 6.220322 141.1725 at 20iterations 3.636735 69.27442 at 30iterations 2.126095 51.50733 at 40iterations 1.239899 21.00118 at 50iterations 0.7250755 14.33433 at 60iterations 0.4226116 7.776157 at 70iterations 0.2463087 4.483856 at 80iterations 0.1430929 2.430672 at 90iterations 8.3515562E-02 1.513187 at 100iterations 4.8626419E-02 0.8538666 at 110iterations 2.8297763E-02 0.4740467 at 120iterations 1.6488532E-02 0.2916536 at 130iterations 9.6053267E-03 0.1804132 at 140iterations 5.5872914E-03 9.6874237E-02 at 150iterations 3.2498164E-03 6.3854218E-02 at 160iterations 1.8940879E-03 3.1166077E-02 at 170iterations 1.1031314E-03 1.8969536E-02 at 180iterations finished qdiffx linear iterations at : 07:56:28 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 1.1031314E-03 1.8969536E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 07:56:29 13.877u 0.275s 0:14.42 98.0% 0+0k 0+0io 0pf+0w