Mon Oct 10 14:24:30 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 Mon Oct 10 2011 at 14:24:31 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 0.6040861 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 0.6040861 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 356.7722 centred at (gu) : 89.77036 90.38595 89.94953 assigned negative charge : -356.7725 centred at (gu) : 89.61242 90.22946 89.91536 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5998 nv = 96 ne = 84 npr = 48436 no. pairs analyzed = 48436 no. exposed pairs = 3287 no. arc points = 23314 no. surface atoms = 1104 nbur = 1325 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3042 m= 0 mr = 15 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2700000 number of dielectric boundary points 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2336 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7340 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3199628E-09 1.2817442E-09 midg,1,midg; midg,igrid,midg -5.5494214E-09 6.3953269E-09 1,midg,midg; igrid,midg,midg -6.4535746E-09 5.6017528E-09 gauss-seidel spectral radius is 0.9858089 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 14:24:31 rms-change max change #iterations 0.1032052 17.19372 at 10iterations 8.8713598E-03 1.344103 at 20iterations 7.5472984E-04 0.1173859 at 30iterations 6.5167886E-05 1.1546612E-02 at 40iterations 5.6155695E-06 7.9727173E-04 at 50iterations finished qdiffx linear iterations at : 14:24:34 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 5.6155695E-06 7.9727173E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 14:24:35 3.281u 0.201s 0:04.01 86.7% 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 Mon Oct 10 2011 at 14:24:35 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 1.812258 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 1.812258 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 356.7722 centred at (gu) : 89.31053 91.15747 89.84803 assigned negative charge : -356.7725 centred at (gu) : 88.83699 90.68835 89.74587 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23314 grid for indexing accessible points = 1.400000 m= 21774 mr = 43270 m= 2694 mr = 15032 m= 116 mr = 1352 m= 0 mr = 35 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 759 time to turn everything in is 0.4700000 number of dielectric boundary points 30086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 17744 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) : 0.6040861 object centre at (A) : -1.785999 5.441998 -11.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2751291E-03 3.7542041E-03 midg,1,midg; midg,igrid,midg 2.8254085E-03 1.0601417E-02 1,midg,midg; igrid,midg,midg -1.6838625E-02 4.5770188E-03 gauss-seidel spectral radius is 0.9984860 estimated iterations to convergence 204 setup time was (sec) 0.7400000 now iterating at: 14:24:36 rms-change max change #iterations 3.659844 170.2693 at 10iterations 1.627032 66.52125 at 20iterations 0.7329244 30.85230 at 30iterations 0.3272769 11.19563 at 40iterations 0.1471509 5.243076 at 50iterations 6.6137068E-02 2.273732 at 60iterations 2.9632108E-02 1.009709 at 70iterations 1.3357721E-02 0.4801331 at 80iterations 5.9602633E-03 0.2374878 at 90iterations 2.6994981E-03 9.9978447E-02 at 100iterations 1.2116830E-03 4.2298019E-02 at 110iterations 5.4159813E-04 1.8150330E-02 at 120iterations finished qdiffx linear iterations at : 14:24:42 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 5.4159813E-04 1.8150330E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 14:24:43 7.300u 0.209s 0:07.97 94.1% 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 Mon Oct 10 2011 at 14:24:43 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 2.718387 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 2.718387 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 356.7722 centred at (gu) : 88.96563 91.73611 89.77202 assigned negative charge : -356.7725 centred at (gu) : 88.25545 91.03240 89.61871 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 150983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23314 grid for indexing accessible points = 1.400000 m= 72188 mr = 105715 m= 23368 mr = 57193 m= 4435 mr = 17551 m= 474 mr = 2897 m= 25 mr = 266 m= 0 mr = 9 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2482 time to turn everything in is 1.140000 number of dielectric boundary points 67842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 18174 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) : 1.812258 object centre at (A) : -1.785999 5.441998 -11.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1795332 6.9600895E-02 midg,1,midg; midg,igrid,midg 0.1095843 3.0652005E-03 1,midg,midg; igrid,midg,midg -0.2103952 2.1944925E-02 gauss-seidel spectral radius is 0.9992228 estimated iterations to convergence 283 setup time was (sec) 1.440000 now iterating at: 14:24:44 rms-change max change #iterations 8.950084 323.2472 at 10iterations 5.224179 123.0080 at 20iterations 3.008647 76.93834 at 30iterations 1.731000 43.36445 at 40iterations 0.9871907 22.67560 at 50iterations 0.5646263 12.44176 at 60iterations 0.3215537 6.424907 at 70iterations 0.1834885 3.851263 at 80iterations 0.1043273 2.233955 at 90iterations 5.9208408E-02 1.120430 at 100iterations 3.3686008E-02 0.7053299 at 110iterations 1.9068709E-02 0.3838129 at 120iterations 1.0829207E-02 0.2407685 at 130iterations 6.1303442E-03 0.1238308 at 140iterations 3.4799059E-03 6.9306374E-02 at 150iterations 1.9690900E-03 4.1074753E-02 at 160iterations 1.1158041E-03 2.3301244E-02 at 170iterations 6.3188572E-04 1.4906883E-02 at 180iterations finished qdiffx linear iterations at : 14:24:56 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 6.3188572E-04 1.4906883E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 14:24:56 12.813u 0.240s 0:13.39 97.4% 0+0k 0+0io 0pf+0w