Sat Oct 8 11:39:47 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 11:39:47 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5651062 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 0.5651062 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 473.4153 centred at (gu) : 89.47806 92.48648 91.14051 assigned negative charge : -475.9167 centred at (gu) : 89.41082 92.58532 91.04168 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 62500 no. pairs analyzed = 62500 no. exposed pairs = 4574 no. arc points = 33450 no. surface atoms = 1522 nbur = 1696 mkacc time = 0.2100000 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 = 1.512000 m= 273 mr = 3110 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3223 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 8715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2895012E-09 1.4385805E-09 midg,1,midg; midg,igrid,midg 5.9092647E-10 -3.1249245E-09 1,midg,midg; igrid,midg,midg -1.4100159E-09 5.6878330E-10 gauss-seidel spectral radius is 0.9838827 estimated iterations to convergence 65 setup time was (sec) 0.7700000 now iterating at: 11:39:49 rms-change max change #iterations 9.1241069E-02 14.34176 at 10iterations 6.5731583E-03 1.179012 at 20iterations 4.6905424E-04 7.1853638E-02 at 30iterations 3.5342116E-05 5.1994324E-03 at 40iterations 2.6022080E-06 3.9386749E-04 at 50iterations finished qdiffx linear iterations at : 11:39:52 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 2.6022080E-06 3.9386749E-04 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 11:39:53 4.519u 0.436s 0:05.29 93.3% 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 11:39:53 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.695319 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 1.695319 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 473.4153 centred at (gu) : 88.43298 97.45826 93.42030 assigned negative charge : -475.9167 centred at (gu) : 88.23212 97.75533 93.12462 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 75392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33450 grid for indexing accessible points = 1.400000 m= 21306 mr = 47317 m= 2009 mr = 13386 m= 48 mr = 792 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 37260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 23623 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) : 0.5651062 object centre at (A) : 37.88150 -7.119498 -20.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0862363E-02 1.2524453E-02 midg,1,midg; midg,igrid,midg 5.2778679E-03 -1.0286345E-02 1,midg,midg; igrid,midg,midg -1.1819178E-02 3.6546255E-03 gauss-seidel spectral radius is 0.9983661 estimated iterations to convergence 196 setup time was (sec) 1.100000 now iterating at: 11:39:54 rms-change max change #iterations 3.764777 154.6484 at 10iterations 1.634199 62.19989 at 20iterations 0.7057205 23.86596 at 30iterations 0.3067114 11.01242 at 40iterations 0.1329105 4.648468 at 50iterations 5.7639588E-02 1.806159 at 60iterations 2.5128433E-02 0.8461781 at 70iterations 1.0944089E-02 0.3891582 at 80iterations 4.7543999E-03 0.1587017 at 90iterations 2.0713198E-03 7.4083328E-02 at 100iterations 9.0471841E-04 3.4803629E-02 at 110iterations 3.9418033E-04 1.3542175E-02 at 120iterations finished qdiffx linear iterations at : 11:40:03 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 3.9418033E-04 1.3542175E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.35000 DelPhi exited at 11:40:04 10.356u 0.435s 0:11.06 97.4% 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 Sat Oct 8 2011 at 11:40:04 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.542978 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 2.542978 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 473.4153 centred at (gu) : 87.64912 101.1870 95.13018 assigned negative charge : -475.9167 centred at (gu) : 87.34794 101.6329 94.68686 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 174968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33450 grid for indexing accessible points = 1.400000 m= 73968 mr = 117230 m= 19878 mr = 55246 m= 2970 mr = 13886 m= 187 mr = 1665 m= 0 mr = 48 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 83896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 24463 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) : 1.695319 object centre at (A) : 37.88150 -7.119498 -20.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1259506 0.1904471 midg,1,midg; midg,igrid,midg 4.4550773E-02 -7.5826608E-02 1,midg,midg; igrid,midg,midg -0.1068487 -6.1099110E-03 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 2.240000 now iterating at: 11:40:07 rms-change max change #iterations 9.757610 369.6356 at 10iterations 5.776967 145.4633 at 20iterations 3.379626 74.91641 at 30iterations 1.963197 43.35272 at 40iterations 1.130967 24.74453 at 50iterations 0.6503714 15.31377 at 60iterations 0.3732018 7.881925 at 70iterations 0.2135501 4.526329 at 80iterations 0.1219683 2.517505 at 90iterations 6.9384329E-02 1.586647 at 100iterations 3.9588794E-02 0.7924995 at 110iterations 2.2472706E-02 0.4330709 at 120iterations 1.2771553E-02 0.2537689 at 130iterations 7.2402242E-03 0.1413002 at 140iterations 4.1060331E-03 8.2927704E-02 at 150iterations 2.3303151E-03 4.6401978E-02 at 160iterations 1.3237436E-03 2.4726033E-02 at 170iterations 7.5285672E-04 1.4716387E-02 at 180iterations finished qdiffx linear iterations at : 11:40:22 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 7.5285672E-04 1.4716387E-02 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 11:40:22 17.780u 0.483s 0:18.54 98.4% 0+0k 0+0io 0pf+0w