Mon Oct 10 11:01:33 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 11:01:33 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 697 has a net charge of 0.5140 !!! WARNING: ADP 1586 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5288333 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 0.5288333 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.514037 assigned positive charge : 852.2054 centred at (gu) : 90.90441 88.82744 88.85899 assigned negative charge : -843.6990 centred at (gu) : 90.90118 88.81501 88.91450 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9605 nv = 96 ne = 84 npr = 105876 no. pairs analyzed = 105876 no. exposed pairs = 6506 no. arc points = 43552 no. surface atoms = 2182 nbur = 3167 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 386 mr = 5315 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4800000 number of dielectric boundary points 4659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4407 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2684265E-10 -7.3362032E-11 midg,1,midg; midg,igrid,midg 2.3904070E-10 2.5463079E-10 1,midg,midg; igrid,midg,midg 1.9180166E-10 3.5242129E-10 gauss-seidel spectral radius is 0.9817455 estimated iterations to convergence 61 setup time was (sec) 0.7000000 now iterating at: 11:01:34 rms-change max change #iterations 8.8070981E-02 12.85135 at 10iterations 5.6766919E-03 0.7499352 at 20iterations 5.7963212E-04 7.6052666E-02 at 30iterations 2.3510086E-04 3.4488976E-02 at 40iterations 1.2655223E-04 1.8089056E-02 at 50iterations finished qdiffx linear iterations at : 11:01:36 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.2655223E-04 1.8089056E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 11:01:37 3.286u 0.275s 0:04.00 88.7% 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 11:01:37 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 697 has a net charge of 0.5140 !!! WARNING: ADP 1586 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.586500 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 1.586500 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.514037 assigned positive charge : 852.2054 centred at (gu) : 92.71148 86.48070 86.57545 assigned negative charge : -843.6990 centred at (gu) : 92.70352 86.44531 86.74375 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 109485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34491 mr = 78425 m= 3172 mr = 24041 m= 74 mr = 1410 m= 0 mr = 15 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.7300000 number of dielectric boundary points 43331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 545 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 39428 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) : 0.5288333 object centre at (A) : 13.36900 3.546001 13.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3361875E-03 -4.2387366E-02 midg,1,midg; midg,igrid,midg 4.0946268E-03 3.5382390E-03 1,midg,midg; igrid,midg,midg 2.9208658E-02 1.5484320E-02 gauss-seidel spectral radius is 0.9982951 estimated iterations to convergence 192 setup time was (sec) 1.020000 now iterating at: 11:01:38 rms-change max change #iterations 4.498382 171.0587 at 10iterations 1.927723 62.94363 at 20iterations 0.8266175 24.01226 at 30iterations 0.3542576 9.867884 at 40iterations 0.1523268 4.149584 at 50iterations 6.5343298E-02 1.946106 at 60iterations 2.8096968E-02 0.7877140 at 70iterations 1.2147641E-02 0.3539467 at 80iterations 5.2512893E-03 0.1677475 at 90iterations 2.3361086E-03 6.8383217E-02 at 100iterations 1.0964100E-03 3.3319473E-02 at 110iterations 5.9967104E-04 2.1458626E-02 at 120iterations finished qdiffx linear iterations at : 11:01:45 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 5.9967104E-04 2.1458626E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 11:01:46 8.534u 0.269s 0:09.15 96.0% 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 11:01:46 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 697 has a net charge of 0.5140 !!! WARNING: ADP 1586 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.379750 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 2.379750 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.514037 assigned positive charge : 852.2054 centred at (gu) : 94.06677 84.72066 84.86268 assigned negative charge : -843.6990 centred at (gu) : 94.05537 84.66799 85.11560 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 254725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121503 mr = 191168 m= 32682 mr = 97447 m= 4778 mr = 24384 m= 308 mr = 2911 m= 1 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 1114 time to turn everything in is 1.810000 number of dielectric boundary points 97940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 41475 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) : 1.586500 object centre at (A) : 13.36900 3.546001 13.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7902674E-05 -1.103514 midg,1,midg; midg,igrid,midg -4.9206167E-02 6.0315769E-02 1,midg,midg; igrid,midg,midg 0.6064898 0.2270420 gauss-seidel spectral radius is 0.9992183 estimated iterations to convergence 282 setup time was (sec) 2.130000 now iterating at: 11:01:48 rms-change max change #iterations 11.90692 312.5079 at 10iterations 6.955556 150.8094 at 20iterations 4.037608 86.38986 at 30iterations 2.325507 48.76085 at 40iterations 1.337710 26.59597 at 50iterations 0.7666280 15.60466 at 60iterations 0.4377329 9.693779 at 70iterations 0.2498685 4.196018 at 80iterations 0.1423084 2.648151 at 90iterations 8.0887876E-02 1.503866 at 100iterations 4.5998473E-02 0.9016490 at 110iterations 2.6147362E-02 0.5051231 at 120iterations 1.4849758E-02 0.2629929 at 130iterations 8.4248073E-03 0.1298256 at 140iterations 4.7897683E-03 8.8346958E-02 at 150iterations 2.7168484E-03 5.4225922E-02 at 160iterations 1.5453238E-03 2.6367188E-02 at 170iterations 8.8216702E-04 1.4957428E-02 at 180iterations finished qdiffx linear iterations at : 11:02:00 total time elapsed so far: 14.08000 # loops : 180 mean,max change (kT/e) : 8.8216702E-04 1.4957428E-02 energy calculations done at 14.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.23000 DelPhi exited at 11:02:01 14.229u 0.273s 0:14.81 97.8% 0+0k 0+0io 0pf+0w