Mon Oct 10 00:09:09 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 Mon Oct 10 2011 at 00:09:09 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 !!! WARNING: SEP 140 has a net charge of -0.4750 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: 0.6320574 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 0.6320574 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2976 net assigned charge : 1.025010 assigned positive charge : 472.1919 centred at (gu) : 91.01148 90.46475 91.37130 assigned negative charge : -471.1682 centred at (gu) : 90.98377 90.38599 91.30981 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8406 nv = 96 ne = 84 npr = 61652 no. pairs analyzed = 61652 no. exposed pairs = 4033 no. arc points = 29055 no. surface atoms = 1339 nbur = 1782 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4482 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3200000 number of dielectric boundary points 4314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2850 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10176 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4493631E-09 1.0727883E-08 midg,1,midg; midg,igrid,midg -7.2313231E-09 1.0914783E-08 1,midg,midg; igrid,midg,midg -1.7162208E-09 5.1530762E-09 gauss-seidel spectral radius is 0.9870862 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 00:09:09 rms-change max change #iterations 0.1505095 19.76419 at 10iterations 1.4676439E-02 1.994205 at 20iterations 1.4102862E-03 0.1970024 at 30iterations 1.3665301E-04 1.9279480E-02 at 40iterations 1.3572429E-05 1.6708374E-03 at 50iterations finished qdiffx linear iterations at : 00:09:12 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.3572429E-05 1.6708374E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 00:09:12 3.136u 0.140s 0:03.54 92.3% 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 Mon Oct 10 2011 at 00:09:12 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 !!! WARNING: SEP 140 has a net charge of -0.4750 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: 1.896172 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 1.896172 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2976 net assigned charge : 1.025010 assigned positive charge : 472.1919 centred at (gu) : 93.03362 91.39346 94.11329 assigned negative charge : -471.1682 centred at (gu) : 92.95114 91.15773 93.92923 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 91088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29055 grid for indexing accessible points = 1.400000 m= 30805 mr = 62130 m= 4442 mr = 22073 m= 235 mr = 2574 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3108 time to turn everything in is 0.6000000 number of dielectric boundary points 39716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23405 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) : 0.6320574 object centre at (A) : -7.695501 12.10150 13.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3359742E-03 -7.1540242E-04 midg,1,midg; midg,igrid,midg -9.9020987E-04 1.3004861E-02 1,midg,midg; igrid,midg,midg -1.7712271E-02 3.2288299E-03 gauss-seidel spectral radius is 0.9986857 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 00:09:13 rms-change max change #iterations 4.662469 186.5324 at 10iterations 2.210656 64.87195 at 20iterations 1.047256 33.20231 at 30iterations 0.4958268 15.19268 at 40iterations 0.2357962 7.451742 at 50iterations 0.1116964 3.302011 at 60iterations 5.3012695E-02 1.653776 at 70iterations 2.5208170E-02 0.7619989 at 80iterations 1.1954806E-02 0.3366785 at 90iterations 5.6842305E-03 0.1677847 at 100iterations 2.6965295E-03 8.5608006E-02 at 110iterations 1.2815890E-03 3.7097931E-02 at 120iterations finished qdiffx linear iterations at : 00:09:19 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.2815890E-03 3.7097931E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 00:09:20 7.080u 0.178s 0:07.53 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 Mon Oct 10 2011 at 00:09:20 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 !!! WARNING: SEP 140 has a net charge of -0.4750 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: 2.844258 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 2.844258 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2976 net assigned charge : 1.025010 assigned positive charge : 472.1919 centred at (gu) : 94.55040 92.08993 96.16959 assigned negative charge : -471.1682 centred at (gu) : 94.42659 91.73663 95.89371 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 211046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29055 grid for indexing accessible points = 1.400000 m= 101941 mr = 151061 m= 34302 mr = 82334 m= 7694 mr = 26817 m= 1028 mr = 5540 m= 46 mr = 648 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 10349 time to turn everything in is 1.520000 number of dielectric boundary points 89640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 23806 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) : 1.896172 object centre at (A) : -7.695501 12.10150 13.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1189428 -0.1056542 midg,1,midg; midg,igrid,midg 9.2612118E-02 -0.1282794 1,midg,midg; igrid,midg,midg -0.3098279 -5.1350243E-02 gauss-seidel spectral radius is 0.9992975 estimated iterations to convergence 298 setup time was (sec) 1.820000 now iterating at: 00:09:22 rms-change max change #iterations 11.17377 318.0435 at 10iterations 6.734373 140.7856 at 20iterations 4.010969 85.62753 at 30iterations 2.383996 47.82985 at 40iterations 1.406473 27.59044 at 50iterations 0.8286397 15.47208 at 60iterations 0.4875234 8.814717 at 70iterations 0.2854041 5.144716 at 80iterations 0.1676414 2.806905 at 90iterations 9.7989447E-02 1.627529 at 100iterations 5.7311695E-02 1.094671 at 110iterations 3.3460043E-02 0.5472519 at 120iterations 1.9565074E-02 0.3369141 at 130iterations 1.1433493E-02 0.1765747 at 140iterations 6.6771773E-03 0.1194515 at 150iterations 3.8883772E-03 6.0815811E-02 at 160iterations 2.2750890E-03 3.5979509E-02 at 170iterations 1.3265735E-03 2.3313284E-02 at 180iterations finished qdiffx linear iterations at : 00:09:32 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 1.3265735E-03 2.3313284E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 00:09:32 12.149u 0.175s 0:12.70 96.9% 0+0k 0+0io 0pf+0w