Tue Oct 11 02:25:47 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 Tue Oct 11 2011 at 02:25:47 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6649110 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 0.6649110 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2591 net assigned charge : 5.420027 assigned positive charge : 421.6773 centred at (gu) : 90.78422 90.30791 90.20644 assigned negative charge : -416.2583 centred at (gu) : 90.60032 90.48323 90.25199 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8137 nv = 96 ne = 84 npr = 54974 no. pairs analyzed = 54974 no. exposed pairs = 3375 no. arc points = 23312 no. surface atoms = 1124 nbur = 1594 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4645 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3000000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2212 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9501 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5393533E-08 4.7424082E-09 midg,1,midg; midg,igrid,midg 5.3443046E-08 -2.9261821E-08 1,midg,midg; igrid,midg,midg -2.4888728E-08 6.9435650E-08 gauss-seidel spectral radius is 0.9882854 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 02:25:48 rms-change max change #iterations 0.1779763 24.74413 at 10iterations 2.0495035E-02 2.757305 at 20iterations 3.3704042E-03 0.5657768 at 30iterations 1.0437205E-03 0.2144852 at 40iterations 4.0065451E-04 8.4068298E-02 at 50iterations finished qdiffx linear iterations at : 02:25:51 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 4.0065451E-04 8.4068298E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 02:25:51 3.312u 0.181s 0:03.96 88.1% 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 Tue Oct 11 2011 at 02:25:51 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.994733 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 1.994733 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2591 net assigned charge : 5.420027 assigned positive charge : 421.6773 centred at (gu) : 92.35197 90.92300 90.61835 assigned negative charge : -416.2583 centred at (gu) : 91.80088 91.44963 90.75591 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23312 grid for indexing accessible points = 1.400000 m= 32597 mr = 61322 m= 5583 mr = 24484 m= 397 mr = 3595 m= 9 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1282 time to turn everything in is 0.5900000 number of dielectric boundary points 36106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20513 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) : 0.6649110 object centre at (A) : 43.75500 41.10350 6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7451858E-02 -2.9309895E-02 midg,1,midg; midg,igrid,midg 7.2609752E-02 -2.1974757E-02 1,midg,midg; igrid,midg,midg -1.8665316E-02 6.2930591E-02 gauss-seidel spectral radius is 0.9987631 estimated iterations to convergence 225 setup time was (sec) 0.8700000 now iterating at: 02:25:52 rms-change max change #iterations 4.888080 184.8615 at 10iterations 2.365458 82.75334 at 20iterations 1.148990 33.38514 at 30iterations 0.5579063 16.11346 at 40iterations 0.2723943 7.887281 at 50iterations 0.1318912 3.940704 at 60iterations 6.4345211E-02 1.959702 at 70iterations 3.1698957E-02 0.9894505 at 80iterations 1.5712377E-02 0.4874306 at 90iterations 8.0422414E-03 0.2681236 at 100iterations 4.3030814E-03 0.1706314 at 110iterations 2.4825246E-03 9.8999023E-02 at 120iterations finished qdiffx linear iterations at : 02:25:59 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.4825246E-03 9.8999023E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 02:26:00 7.774u 0.233s 0:08.31 96.2% 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 Tue Oct 11 2011 at 02:26:00 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2718 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.992100 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): 20.52800 66.98200 ymin,ymax (A): 14.33300 67.87400 zmin,zma (A): -17.36600 30.67800 x,y,z range (A): 46.45400 53.54100 48.04400 scale (grids/A): 2.992100 object centre (A): 43.75500 41.10350 6.656000 number of atom coordinates read : 2718 total number of charged atoms : 2591 net assigned charge : 5.420027 assigned positive charge : 421.6773 centred at (gu) : 93.52780 91.38436 90.92751 assigned negative charge : -416.2583 centred at (gu) : 92.70123 92.17439 91.13366 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 201138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23312 grid for indexing accessible points = 1.400000 m= 104270 mr = 148325 m= 39461 mr = 86105 m= 10290 mr = 32204 m= 1683 mr = 7861 m= 144 mr = 1177 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 4381 time to turn everything in is 1.580000 number of dielectric boundary points 81234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 20727 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) : 1.994733 object centre at (A) : 43.75500 41.10350 6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2297772 -0.3340340 midg,1,midg; midg,igrid,midg 0.9880593 -0.3463815 1,midg,midg; igrid,midg,midg -0.2086402 0.5002934 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 1.890000 now iterating at: 02:26:02 rms-change max change #iterations 11.23619 418.8986 at 10iterations 6.631511 154.7812 at 20iterations 3.905926 81.02879 at 30iterations 2.298309 40.17582 at 40iterations 1.350667 26.22075 at 50iterations 0.7920588 14.06564 at 60iterations 0.4630132 8.743977 at 70iterations 0.2710171 4.674139 at 80iterations 0.1585038 2.798046 at 90iterations 9.2557617E-02 1.687817 at 100iterations 5.4259703E-02 0.9502182 at 110iterations 3.1824753E-02 0.5484543 at 120iterations 1.8718302E-02 0.3801441 at 130iterations 1.1172823E-02 0.2205315 at 140iterations 6.8227821E-03 0.1376686 at 150iterations 4.3286630E-03 9.4726563E-02 at 160iterations 2.9176346E-03 6.9709778E-02 at 170iterations 2.0972998E-03 5.2192688E-02 at 180iterations finished qdiffx linear iterations at : 02:26:12 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 2.0972998E-03 5.2192688E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 02:26:12 12.110u 0.242s 0:12.71 97.1% 0+0k 0+0io 0pf+0w