Sat Oct 8 22:51:15 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 Sat Oct 8 2011 at 22:51:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2238 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6470845 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): -13.23700 40.44400 ymin,ymax (A): -31.34100 23.67500 zmin,zma (A): -9.654000 34.35400 x,y,z range (A): 53.68100 55.01600 44.00800 scale (grids/A): 0.6470845 object centre (A): 13.60350 -3.833000 12.35000 number of atom coordinates read : 2238 total number of charged atoms : 2105 net assigned charge : 11.50002 assigned positive charge : 323.9427 centred at (gu) : 89.09894 91.96533 90.87478 assigned negative charge : -312.4432 centred at (gu) : 89.05477 92.04391 90.77050 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6544 nv = 96 ne = 84 npr = 44080 no. pairs analyzed = 44080 no. exposed pairs = 3043 no. arc points = 21824 no. surface atoms = 1014 nbur = 1224 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3324 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.1700000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7654 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2894712E-09 3.8621426E-08 midg,1,midg; midg,igrid,midg 1.9567558E-08 1.7014996E-08 1,midg,midg; igrid,midg,midg 1.8571484E-08 2.1160142E-08 gauss-seidel spectral radius is 0.9876049 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 22:51:15 rms-change max change #iterations 0.1312483 22.74198 at 10iterations 1.3214451E-02 2.019423 at 20iterations 1.3190327E-03 0.2038345 at 30iterations 1.4364820E-04 2.0801544E-02 at 40iterations 1.7941789E-05 2.8629303E-03 at 50iterations finished qdiffx linear iterations at : 22:51:18 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.7941789E-05 2.8629303E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 22:51:19 3.478u 0.202s 0:03.95 92.9% 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 Sat Oct 8 2011 at 22:51:19 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 = 2238 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: 1.941254 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): -13.23700 40.44400 ymin,ymax (A): -31.34100 23.67500 zmin,zma (A): -9.654000 34.35400 x,y,z range (A): 53.68100 55.01600 44.00800 scale (grids/A): 1.941254 object centre (A): 13.60350 -3.833000 12.35000 number of atom coordinates read : 2238 total number of charged atoms : 2105 net assigned charge : 11.50002 assigned positive charge : 323.9427 centred at (gu) : 87.29659 95.89584 92.62417 assigned negative charge : -312.4432 centred at (gu) : 87.16442 96.13180 92.31152 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 24953 mr = 46195 m= 4257 mr = 17873 m= 319 mr = 2537 m= 6 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1362 time to turn everything in is 0.3500000 number of dielectric boundary points 32583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16574 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) : 0.6470845 object centre at (A) : 13.60350 -3.833000 12.35000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4298157E-03 2.8223826E-02 midg,1,midg; midg,igrid,midg 4.7793590E-02 2.6088504E-02 1,midg,midg; igrid,midg,midg 6.3676886E-02 5.1804259E-02 gauss-seidel spectral radius is 0.9986618 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 22:51:20 rms-change max change #iterations 3.912883 231.1099 at 10iterations 1.839299 77.37920 at 20iterations 0.8666620 30.88779 at 30iterations 0.4065537 14.30423 at 40iterations 0.1917196 6.381031 at 50iterations 9.0316691E-02 2.886057 at 60iterations 4.2525325E-02 1.390587 at 70iterations 2.0006476E-02 0.6815186 at 80iterations 9.4387149E-03 0.3051815 at 90iterations 4.4546481E-03 0.1406407 at 100iterations 2.1028819E-03 6.8355560E-02 at 110iterations 9.8628353E-04 3.2249451E-02 at 120iterations finished qdiffx linear iterations at : 22:51:27 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 9.8628353E-04 3.2249451E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 22:51:28 8.113u 0.228s 0:08.66 96.1% 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 22:51:28 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 = 2238 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: 2.911880 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): -13.23700 40.44400 ymin,ymax (A): -31.34100 23.67500 zmin,zma (A): -9.654000 34.35400 x,y,z range (A): 53.68100 55.01600 44.00800 scale (grids/A): 2.911880 object centre (A): 13.60350 -3.833000 12.35000 number of atom coordinates read : 2238 total number of charged atoms : 2105 net assigned charge : 11.50002 assigned positive charge : 323.9427 centred at (gu) : 85.94493 98.84375 93.93613 assigned negative charge : -312.4432 centred at (gu) : 85.74673 99.19784 93.46740 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 79685 mr = 112531 m= 29641 mr = 63564 m= 7564 mr = 23250 m= 1202 mr = 5520 m= 114 mr = 804 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4601 time to turn everything in is 0.9200000 number of dielectric boundary points 73527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 16840 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) : 1.941254 object centre at (A) : 13.60350 -3.833000 12.35000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2962510E-02 0.2557008 midg,1,midg; midg,igrid,midg 0.5629101 0.3154080 1,midg,midg; igrid,midg,midg 0.6459457 0.5019982 gauss-seidel spectral radius is 0.9992724 estimated iterations to convergence 293 setup time was (sec) 1.170000 now iterating at: 22:51:29 rms-change max change #iterations 9.326476 472.3672 at 10iterations 5.519903 150.9709 at 20iterations 3.236553 88.30327 at 30iterations 1.899693 57.75286 at 40iterations 1.108354 22.66674 at 50iterations 0.6439443 13.48184 at 60iterations 0.3748049 8.507668 at 70iterations 0.2175941 4.157829 at 80iterations 0.1260542 3.018638 at 90iterations 7.2963320E-02 1.522804 at 100iterations 4.2251635E-02 0.8107843 at 110iterations 2.4519715E-02 0.4711685 at 120iterations 1.4148206E-02 0.2580376 at 130iterations 8.1686312E-03 0.1467388 at 140iterations 4.7343653E-03 8.9352608E-02 at 150iterations 2.7352679E-03 5.6175709E-02 at 160iterations 1.5793301E-03 2.8907776E-02 at 170iterations 9.1523456E-04 1.6827106E-02 at 180iterations finished qdiffx linear iterations at : 22:51:41 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 9.1523456E-04 1.6827106E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 22:51:41 13.185u 0.233s 0:13.68 98.0% 0+0k 0+0io 0pf+0w