Sat Oct 15 12:28:55 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 15 2011 at 12:28:55 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6624981 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): -24.25600 25.67700 ymin,ymax (A): 0.8400000 45.69100 zmin,zma (A): -23.50100 30.23500 x,y,z range (A): 49.93300 44.85100 53.73600 scale (grids/A): 0.6624981 object centre (A): 0.7104998 23.26550 3.367000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 302.0560 centred at (gu) : 89.25146 89.66750 88.35696 assigned negative charge : -304.5561 centred at (gu) : 89.19479 89.86835 88.33324 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5853 nv = 96 ne = 84 npr = 42092 no. pairs analyzed = 42092 no. exposed pairs = 2511 no. arc points = 17653 no. surface atoms = 843 nbur = 1158 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 3181 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2900000 number of dielectric boundary points 2923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4917088E-08 -2.0808755E-09 midg,1,midg; midg,igrid,midg 2.7628339E-08 -3.7818996E-08 1,midg,midg; igrid,midg,midg -1.8822687E-08 2.1563755E-09 gauss-seidel spectral radius is 0.9881353 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 12:28:56 rms-change max change #iterations 0.1512090 25.96871 at 10iterations 1.5944708E-02 2.354000 at 20iterations 1.7343326E-03 0.2734451 at 30iterations 1.8193196E-04 2.8514862E-02 at 40iterations 1.9547690E-05 3.0619502E-03 at 50iterations finished qdiffx linear iterations at : 12:28:59 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.9547690E-05 3.0619502E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 12:28:59 3.660u 0.213s 0:04.32 89.5% 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 12:28:59 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.987494 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): -24.25600 25.67700 ymin,ymax (A): 0.8400000 45.69100 zmin,zma (A): -23.50100 30.23500 x,y,z range (A): 49.93300 44.85100 53.73600 scale (grids/A): 1.987494 object centre (A): 0.7104998 23.26550 3.367000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 302.0560 centred at (gu) : 87.75436 89.00248 85.07101 assigned negative charge : -304.5561 centred at (gu) : 87.58455 89.60518 84.99978 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17653 grid for indexing accessible points = 1.400000 m= 22022 mr = 43456 m= 3454 mr = 16181 m= 207 mr = 2139 m= 5 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1084 time to turn everything in is 0.5000000 number of dielectric boundary points 27010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14703 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) : 0.6624981 object centre at (A) : 0.7104998 23.26550 3.367000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8286397E-02 1.3379465E-02 midg,1,midg; midg,igrid,midg 4.5659989E-02 -2.7936706E-02 1,midg,midg; igrid,midg,midg -4.2189825E-02 -4.5635812E-03 gauss-seidel spectral radius is 0.9986804 estimated iterations to convergence 218 setup time was (sec) 0.8200000 now iterating at: 12:29:00 rms-change max change #iterations 4.084331 223.6677 at 10iterations 1.927809 68.97922 at 20iterations 0.9130133 32.41207 at 30iterations 0.4355780 16.28899 at 40iterations 0.2058647 8.055414 at 50iterations 9.6926436E-02 3.234543 at 60iterations 4.6257701E-02 1.601883 at 70iterations 2.1838402E-02 0.8211927 at 80iterations 1.0327217E-02 0.3310585 at 90iterations 4.9365521E-03 0.1626329 at 100iterations 2.3340206E-03 8.3831787E-02 at 110iterations 1.1109923E-03 3.7837982E-02 at 120iterations finished qdiffx linear iterations at : 12:29:07 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.1109923E-03 3.7837982E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 12:29:08 8.097u 0.256s 0:08.72 95.6% 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 12:29:08 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.981242 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): -24.25600 25.67700 ymin,ymax (A): 0.8400000 45.69100 zmin,zma (A): -23.50100 30.23500 x,y,z range (A): 49.93300 44.85100 53.73600 scale (grids/A): 2.981242 object centre (A): 0.7104998 23.26550 3.367000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 302.0560 centred at (gu) : 86.63146 88.50372 82.60650 assigned negative charge : -304.5561 centred at (gu) : 86.37685 89.40778 82.49976 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 146004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17653 grid for indexing accessible points = 1.400000 m= 71954 mr = 105200 m= 25234 mr = 58904 m= 6190 mr = 20084 m= 962 mr = 4602 m= 64 mr = 614 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 3589 time to turn everything in is 1.290000 number of dielectric boundary points 60976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 14896 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) : 1.987494 object centre at (A) : 0.7104998 23.26550 3.367000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5487194 0.4879953 midg,1,midg; midg,igrid,midg 0.5078567 -0.2953360 1,midg,midg; igrid,midg,midg -0.3942988 3.2716587E-03 gauss-seidel spectral radius is 0.9992602 estimated iterations to convergence 290 setup time was (sec) 1.640000 now iterating at: 12:29:10 rms-change max change #iterations 9.389138 373.0601 at 10iterations 5.399655 126.4124 at 20iterations 3.113975 75.04291 at 30iterations 1.792876 37.19794 at 40iterations 1.028317 21.26411 at 50iterations 0.5916081 12.87302 at 60iterations 0.3389228 6.292603 at 70iterations 0.1946737 3.672601 at 80iterations 0.1114013 2.036507 at 90iterations 6.3955277E-02 1.347450 at 100iterations 3.6740016E-02 0.7293596 at 110iterations 2.1097630E-02 0.4023625 at 120iterations 1.2101980E-02 0.2344093 at 130iterations 6.9436012E-03 0.1453214 at 140iterations 3.9827959E-03 8.3237171E-02 at 150iterations 2.2883082E-03 4.3987274E-02 at 160iterations 1.3133403E-03 2.4783611E-02 at 170iterations 7.5625104E-04 1.5216827E-02 at 180iterations finished qdiffx linear iterations at : 12:29:23 total time elapsed so far: 14.56000 # loops : 180 mean,max change (kT/e) : 7.5625104E-04 1.5216827E-02 energy calculations done at 14.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.75000 DelPhi exited at 12:29:23 14.752u 0.249s 0:15.36 97.5% 0+0k 0+0io 0pf+0w