Tue Oct 11 02:43:48 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 Tue Oct 11 2011 at 02:43:48 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6673540 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 0.6673540 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2615 net assigned charge : 9.000009 assigned positive charge : 423.5764 centred at (gu) : 89.72819 89.86772 90.79677 assigned negative charge : -414.5775 centred at (gu) : 89.88390 89.73588 90.83364 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8246 nv = 96 ne = 84 npr = 55683 no. pairs analyzed = 55683 no. exposed pairs = 3396 no. arc points = 23223 no. surface atoms = 1140 nbur = 1609 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4689 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3900000 number of dielectric boundary points 3954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2208 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1765691E-08 2.1572472E-08 midg,1,midg; midg,igrid,midg -6.3377823E-09 5.9392605E-08 1,midg,midg; igrid,midg,midg 7.0766063E-08 -1.1609580E-08 gauss-seidel spectral radius is 0.9883740 estimated iterations to convergence 76 setup time was (sec) 0.7000000 now iterating at: 02:43:49 rms-change max change #iterations 0.1832211 22.57497 at 10iterations 2.0936280E-02 3.061104 at 20iterations 3.3215596E-03 0.5761337 at 30iterations 1.0013732E-03 0.2105026 at 40iterations 3.7257848E-04 7.9956055E-02 at 50iterations finished qdiffx linear iterations at : 02:43:52 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 3.7257848E-04 7.9956055E-02 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 02:43:53 4.116u 0.177s 0:04.83 88.6% 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 Tue Oct 11 2011 at 02:43:53 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! 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: 2.002062 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 2.002062 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2615 net assigned charge : 9.000009 assigned positive charge : 423.5764 centred at (gu) : 89.18393 89.60223 92.38960 assigned negative charge : -414.5775 centred at (gu) : 89.65162 89.20710 92.50064 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 89190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23223 grid for indexing accessible points = 1.400000 m= 33789 mr = 63029 m= 5933 mr = 25594 m= 412 mr = 3958 m= 3 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3550 time to turn everything in is 0.8000000 number of dielectric boundary points 36583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20686 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) : 0.6673540 object centre at (A) : 1.172500 37.34250 6.289000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3205372E-02 -2.0187978E-02 midg,1,midg; midg,igrid,midg -1.3587552E-02 7.7901654E-02 1,midg,midg; igrid,midg,midg 7.1356215E-02 2.3699630E-02 gauss-seidel spectral radius is 0.9987775 estimated iterations to convergence 226 setup time was (sec) 1.140000 now iterating at: 02:43:54 rms-change max change #iterations 4.887015 252.8899 at 10iterations 2.381798 77.97070 at 20iterations 1.163157 34.13092 at 30iterations 0.5658711 15.82829 at 40iterations 0.2762157 7.477142 at 50iterations 0.1345023 3.776990 at 60iterations 6.6156104E-02 2.016942 at 70iterations 3.2532386E-02 1.016022 at 80iterations 1.6233997E-02 0.4731140 at 90iterations 8.2568182E-03 0.2640266 at 100iterations 4.3686582E-03 0.1565933 at 110iterations 2.4560080E-03 9.8632813E-02 at 120iterations finished qdiffx linear iterations at : 02:44:02 total time elapsed so far: 9.060000 # loops : 120 mean,max change (kT/e) : 2.4560080E-03 9.8632813E-02 energy calculations done at 9.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 02:44:03 9.294u 0.195s 0:10.22 92.7% 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 Tue Oct 11 2011 at 02:44:03 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! 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: 3.003093 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 3.003093 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2615 net assigned charge : 9.000009 assigned positive charge : 423.5764 centred at (gu) : 88.77579 89.40321 93.58421 assigned negative charge : -414.5775 centred at (gu) : 89.47737 88.81046 93.75088 start vw surface at 0.1900000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 205992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23223 grid for indexing accessible points = 1.400000 m= 107591 mr = 152291 m= 41574 mr = 89355 m= 11016 mr = 34039 m= 1813 mr = 8565 m= 130 mr = 1301 m= 0 mr = 68 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 11646 time to turn everything in is 2.060000 number of dielectric boundary points 82497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 20919 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) : 2.002062 object centre at (A) : 1.172500 37.34250 6.289000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1848240 -0.2456259 midg,1,midg; midg,igrid,midg -0.3391912 1.026265 1,midg,midg; igrid,midg,midg 0.6857827 0.2633172 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 2.420000 now iterating at: 02:44:06 rms-change max change #iterations 11.17163 461.7896 at 10iterations 6.587329 139.1566 at 20iterations 3.881278 73.84751 at 30iterations 2.281085 43.94270 at 40iterations 1.340963 22.86595 at 50iterations 0.7849909 13.88191 at 60iterations 0.4603398 7.931648 at 70iterations 0.2693847 4.406940 at 80iterations 0.1575809 2.950317 at 90iterations 9.2235968E-02 1.643698 at 100iterations 5.4083548E-02 0.9347153 at 110iterations 3.1724907E-02 0.5375443 at 120iterations 1.8699864E-02 0.3277054 at 130iterations 1.1125861E-02 0.2333908 at 140iterations 6.7617921E-03 0.1468544 at 150iterations 4.2507923E-03 9.2575073E-02 at 160iterations 2.8133430E-03 6.4743042E-02 at 170iterations 1.9821769E-03 4.9896240E-02 at 180iterations finished qdiffx linear iterations at : 02:44:18 total time elapsed so far: 14.73000 # loops : 180 mean,max change (kT/e) : 1.9821769E-03 4.9896240E-02 energy calculations done at 14.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.98000 DelPhi exited at 02:44:19 14.978u 0.210s 0:15.72 96.5% 0+0k 0+0io 0pf+0w