Sat Oct 15 14:24:07 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 15 2011 at 14:24:07 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 = 3358 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: 0.6483455 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 0.6483455 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.1885 centred at (gu) : 89.27336 90.88892 89.41210 assigned negative charge : -512.1895 centred at (gu) : 89.30263 90.81626 89.42896 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9347 nv = 96 ne = 84 npr = 69347 no. pairs analyzed = 69347 no. exposed pairs = 3740 no. arc points = 25773 no. surface atoms = 1272 nbur = 2086 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 5612 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.3900000 number of dielectric boundary points 4220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2489 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 11270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5261169E-09 -1.4072421E-09 midg,1,midg; midg,igrid,midg -1.0273826E-08 1.8791704E-08 1,midg,midg; igrid,midg,midg 8.4743261E-09 -3.4173475E-09 gauss-seidel spectral radius is 0.9877301 estimated iterations to convergence 74 setup time was (sec) 0.6900000 now iterating at: 14:24:08 rms-change max change #iterations 0.1829938 23.19994 at 10iterations 1.9042779E-02 2.171928 at 20iterations 2.2901946E-03 0.3114729 at 30iterations 5.4584316E-04 8.1115723E-02 at 40iterations 2.3176517E-04 3.4387589E-02 at 50iterations finished qdiffx linear iterations at : 14:24:12 total time elapsed so far: 5.260000 # loops : 50 mean,max change (kT/e) : 2.3176517E-04 3.4387589E-02 energy calculations done at 5.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.430000 DelPhi exited at 14:24:13 5.434u 0.457s 0:06.15 95.6% 0+0k 0+0io 6pf+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 15 2011 at 14:24:13 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 = 3358 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.945036 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 1.945036 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.1885 centred at (gu) : 87.81945 92.66576 88.23524 assigned negative charge : -512.1895 centred at (gu) : 87.90728 92.44852 88.28632 start vw surface at 0.1300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 101239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25773 grid for indexing accessible points = 1.400000 m= 39701 mr = 74069 m= 6647 mr = 30560 m= 433 mr = 4328 m= 11 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1621 time to turn everything in is 0.8400000 number of dielectric boundary points 38897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 25273 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) : 0.6483455 object centre at (A) : 37.41800 -15.19150 58.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7757123E-03 -2.0081304E-02 midg,1,midg; midg,igrid,midg -8.9308564E-03 3.3183217E-02 1,midg,midg; igrid,midg,midg 1.4124178E-02 4.2737436E-02 gauss-seidel spectral radius is 0.9987485 estimated iterations to convergence 224 setup time was (sec) 1.200000 now iterating at: 14:24:15 rms-change max change #iterations 5.163598 173.1207 at 10iterations 2.505344 69.63661 at 20iterations 1.222122 35.02921 at 30iterations 0.5928515 17.89933 at 40iterations 0.2877269 7.690948 at 50iterations 0.1400827 3.586928 at 60iterations 6.8106726E-02 1.786505 at 70iterations 3.3055559E-02 0.9116631 at 80iterations 1.6053123E-02 0.4396324 at 90iterations 7.8482311E-03 0.2197647 at 100iterations 3.8848580E-03 0.1137557 at 110iterations 1.9494969E-03 5.9311390E-02 at 120iterations finished qdiffx linear iterations at : 14:24:27 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 1.9494969E-03 5.9311390E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 14:24:27 13.388u 0.551s 0:14.37 96.9% 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 15 2011 at 14:24:27 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 = 3358 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.917555 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 2.917555 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.1885 centred at (gu) : 86.72891 93.99880 87.35275 assigned negative charge : -512.1895 centred at (gu) : 86.86076 93.67267 87.42931 start vw surface at 0.1500000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 233748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25773 grid for indexing accessible points = 1.400000 m= 126996 mr = 177898 m= 48730 mr = 107027 m= 12327 mr = 40316 m= 1948 mr = 9471 m= 140 mr = 1274 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 5447 time to turn everything in is 2.310000 number of dielectric boundary points 87835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 25679 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) : 1.945036 object centre at (A) : 37.41800 -15.19150 58.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2870059E-02 -7.4110419E-02 midg,1,midg; midg,igrid,midg -9.2416257E-02 0.3837960 1,midg,midg; igrid,midg,midg 0.1709423 0.5203707 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 2.740000 now iterating at: 14:24:31 rms-change max change #iterations 11.92287 447.5997 at 10iterations 7.092777 147.7830 at 20iterations 4.207767 88.77982 at 30iterations 2.487758 50.94462 at 40iterations 1.466589 26.33926 at 50iterations 0.8619509 15.43484 at 60iterations 0.5075955 8.554678 at 70iterations 0.2974134 5.334780 at 80iterations 0.1743367 3.001434 at 90iterations 0.1019693 1.504116 at 100iterations 5.9749745E-02 0.9121704 at 110iterations 3.4886274E-02 0.5618744 at 120iterations 2.0415483E-02 0.3427215 at 130iterations 1.1938324E-02 0.1891801 at 140iterations 6.9861216E-03 0.1028004 at 150iterations 4.0863608E-03 6.3488007E-02 at 160iterations 2.3907537E-03 3.6792755E-02 at 170iterations 1.4037624E-03 2.1851361E-02 at 180iterations finished qdiffx linear iterations at : 14:24:51 total time elapsed so far: 23.55000 # loops : 180 mean,max change (kT/e) : 1.4037624E-03 2.1851361E-02 energy calculations done at 23.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.73000 DelPhi exited at 14:24:52 23.730u 0.555s 0:24.78 97.9% 0+0k 0+0io 0pf+0w