Sat Oct 8 20:26:40 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 Sat Oct 8 2011 at 20:26:40 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 0.6250658 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 0.6250658 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 88.64242 89.36203 89.85365 assigned negative charge : -391.6796 centred at (gu) : 88.54033 89.40048 89.75182 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6776 nv = 96 ne = 84 npr = 52909 no. pairs analyzed = 52909 no. exposed pairs = 3089 no. arc points = 22222 no. surface atoms = 1028 nbur = 1561 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3783 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.3500000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2220 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2099049E-09 1.1334458E-08 midg,1,midg; midg,igrid,midg 7.8938021E-09 8.2065299E-10 1,midg,midg; igrid,midg,midg -5.6333969E-09 8.7288932E-09 gauss-seidel spectral radius is 0.9867421 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 20:26:41 rms-change max change #iterations 0.1298658 18.68789 at 10iterations 1.2436789E-02 1.797186 at 20iterations 1.1696443E-03 0.1666040 at 30iterations 1.1621922E-04 1.8341064E-02 at 40iterations 1.2070042E-05 1.8615723E-03 at 50iterations finished qdiffx linear iterations at : 20:26:44 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.2070042E-05 1.8615723E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 20:26:45 4.178u 0.273s 0:04.87 91.1% 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 Sat Oct 8 2011 at 20:26:45 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 1.875197 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 1.875197 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 85.92692 88.08552 89.56048 assigned negative charge : -391.6796 centred at (gu) : 85.62067 88.20116 89.25536 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 26364 mr = 51501 m= 3780 mr = 19674 m= 199 mr = 2285 m= 0 mr = 56 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 4465 time to turn everything in is 0.6400000 number of dielectric boundary points 30305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19369 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) : 0.6250658 object centre at (A) : 14.12150 1.133000 16.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9879691E-02 2.3363257E-02 midg,1,midg; midg,igrid,midg 1.1814339E-02 2.5469917E-03 1,midg,midg; igrid,midg,midg -2.6437780E-03 3.6273323E-02 gauss-seidel spectral radius is 0.9985920 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 20:26:46 rms-change max change #iterations 4.109775 163.6214 at 10iterations 1.902611 80.21184 at 20iterations 0.8801438 27.15583 at 30iterations 0.4070993 13.86905 at 40iterations 0.1888000 6.077131 at 50iterations 8.7554157E-02 2.728958 at 60iterations 4.0524550E-02 1.280079 at 70iterations 1.8770969E-02 0.6363640 at 80iterations 8.6882506E-03 0.2686234 at 90iterations 4.0192925E-03 0.1378670 at 100iterations 1.8644367E-03 6.4495087E-02 at 110iterations 8.6279021E-04 2.9453278E-02 at 120iterations finished qdiffx linear iterations at : 20:26:55 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 8.6279021E-04 2.9453278E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 20:26:55 9.620u 0.317s 0:10.23 97.0% 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 20:26:55 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 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: 2.812796 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): -10.75600 38.99900 ymin,ymax (A): -21.89300 24.15900 zmin,zma (A): -12.45000 44.50400 x,y,z range (A): 49.75500 46.05200 56.95400 scale (grids/A): 2.812796 object centre (A): 14.12150 1.133000 16.02700 number of atom coordinates read : 2589 total number of charged atoms : 2465 net assigned charge : 4.042008 assigned positive charge : 395.7209 centred at (gu) : 83.89020 87.12801 89.34070 assigned negative charge : -391.6796 centred at (gu) : 83.43101 87.30164 88.88312 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 169952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22222 grid for indexing accessible points = 1.400000 m= 86110 mr = 124357 m= 30049 mr = 71306 m= 6746 mr = 24121 m= 839 mr = 4989 m= 46 mr = 529 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 14596 time to turn everything in is 1.650000 number of dielectric boundary points 68430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19714 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) : 1.875197 object centre at (A) : 14.12150 1.133000 16.02700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1773384 0.2608072 midg,1,midg; midg,igrid,midg 0.1339007 1.2489474E-02 1,midg,midg; igrid,midg,midg -1.6706496E-02 0.4651852 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.980000 now iterating at: 20:26:58 rms-change max change #iterations 9.644978 322.3602 at 10iterations 5.570152 127.7269 at 20iterations 3.191134 75.30489 at 30iterations 1.827991 38.67899 at 40iterations 1.045297 21.15008 at 50iterations 0.5967953 11.89498 at 60iterations 0.3404196 6.248757 at 70iterations 0.1951554 3.606493 at 80iterations 0.1110061 1.952749 at 90iterations 6.3426003E-02 1.187026 at 100iterations 3.6170918E-02 0.6825824 at 110iterations 2.0639075E-02 0.4136333 at 120iterations 1.1770181E-02 0.2205925 at 130iterations 6.7416830E-03 0.1300240 at 140iterations 3.8377084E-03 7.0678711E-02 at 150iterations 2.1915112E-03 4.1536331E-02 at 160iterations 1.2547415E-03 2.3698807E-02 at 170iterations 7.1748777E-04 1.3502121E-02 at 180iterations finished qdiffx linear iterations at : 20:27:12 total time elapsed so far: 16.00000 # loops : 180 mean,max change (kT/e) : 7.1748777E-04 1.3502121E-02 energy calculations done at 16.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.18000 DelPhi exited at 20:27:12 16.177u 0.324s 0:16.82 98.0% 0+0k 0+0io 0pf+0w