Sun Oct 9 12:30:51 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 12:30:51 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 = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6956657 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): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 0.6956657 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4590 centred at (gu) : 89.28805 90.99995 90.93906 assigned negative charge : -362.9596 centred at (gu) : 89.25745 91.19235 91.03087 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7801 nv = 96 ne = 84 npr = 48385 no. pairs analyzed = 48385 no. exposed pairs = 2964 no. arc points = 20700 no. surface atoms = 992 nbur = 1410 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4357 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.1800000 number of dielectric boundary points 3841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1903 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2960601E-08 -2.0773246E-08 midg,1,midg; midg,igrid,midg 8.7435581E-08 -7.6831952E-08 1,midg,midg; igrid,midg,midg 1.1713309E-08 3.2376541E-08 gauss-seidel spectral radius is 0.9892634 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 12:30:51 rms-change max change #iterations 0.2036738 27.62059 at 10iterations 2.5241537E-02 3.406219 at 20iterations 3.5574937E-03 0.5508652 at 30iterations 7.8707823E-04 0.1310043 at 40iterations 2.5741660E-04 4.1641235E-02 at 50iterations finished qdiffx linear iterations at : 12:30:54 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.5741660E-04 4.1641235E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 12:30:55 3.329u 0.164s 0:03.80 91.5% 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 12:30:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.086997 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): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 2.086997 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4590 centred at (gu) : 87.86351 92.99944 92.81662 assigned negative charge : -362.9596 centred at (gu) : 87.77204 93.57674 93.09263 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 31513 mr = 58269 m= 5535 mr = 23505 m= 460 mr = 3515 m= 15 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1054 time to turn everything in is 0.4000000 number of dielectric boundary points 35023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17926 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) : 0.6956657 object centre at (A) : 19.68100 11.56000 23.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0150627E-02 1.6518584E-03 midg,1,midg; midg,igrid,midg 2.2308966E-02 -7.7089489E-02 1,midg,midg; igrid,midg,midg 6.0342032E-02 5.1137954E-03 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.6200000 now iterating at: 12:30:56 rms-change max change #iterations 4.917898 224.9996 at 10iterations 2.414251 83.69898 at 20iterations 1.195226 40.14187 at 30iterations 0.5942829 17.70707 at 40iterations 0.2947968 8.578835 at 50iterations 0.1466459 4.622069 at 60iterations 7.2687283E-02 2.178585 at 70iterations 3.6182653E-02 1.041147 at 80iterations 1.8096993E-02 0.5222178 at 90iterations 9.1398470E-03 0.2696457 at 100iterations 4.6599498E-03 0.1399879 at 110iterations 2.4452766E-03 7.8023911E-02 at 120iterations finished qdiffx linear iterations at : 12:31:03 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.4452766E-03 7.8023911E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 12:31:03 7.747u 0.195s 0:08.22 96.4% 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 12:31:03 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 = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.130496 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): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 3.130496 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500024 assigned positive charge : 366.4590 centred at (gu) : 86.79515 94.49907 94.22480 assigned negative charge : -362.9596 centred at (gu) : 86.65797 95.36508 94.63890 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 191417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 100501 mr = 140287 m= 38196 mr = 82987 m= 10126 mr = 30929 m= 1872 mr = 7648 m= 247 mr = 1367 m= 9 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 3426 time to turn everything in is 1.240000 number of dielectric boundary points 78991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 18078 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) : 2.086997 object centre at (A) : 19.68100 11.56000 23.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5815398 -9.2923589E-02 midg,1,midg; midg,igrid,midg 0.4952061 -0.7716982 1,midg,midg; igrid,midg,midg 0.8452719 -0.1528062 gauss-seidel spectral radius is 0.9993003 estimated iterations to convergence 298 setup time was (sec) 1.470000 now iterating at: 12:31:05 rms-change max change #iterations 10.96395 390.4203 at 10iterations 6.499449 131.8928 at 20iterations 3.838715 75.70490 at 30iterations 2.265684 44.95573 at 40iterations 1.337151 26.91914 at 50iterations 0.7862831 15.88434 at 60iterations 0.4612637 8.169628 at 70iterations 0.2709096 4.839326 at 80iterations 0.1587951 2.922913 at 90iterations 9.3125694E-02 1.594511 at 100iterations 5.4660190E-02 0.8817863 at 110iterations 3.2218963E-02 0.5417156 at 120iterations 1.9126128E-02 0.3265057 at 130iterations 1.1452967E-02 0.2007580 at 140iterations 7.0161889E-03 0.1261368 at 150iterations 4.4626906E-03 9.2628479E-02 at 160iterations 2.9864979E-03 6.1630249E-02 at 170iterations 2.1300460E-03 4.5234680E-02 at 180iterations finished qdiffx linear iterations at : 12:31:16 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.1300460E-03 4.5234680E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 12:31:16 12.941u 0.215s 0:13.49 97.4% 0+0k 0+0io 0pf+0w