Sun Oct 9 08:23:59 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 Sun Oct 9 2011 at 08:23:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5139087 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 0.5139087 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.999940 assigned positive charge : 872.2128 centred at (gu) : 90.30152 91.01608 90.31805 assigned negative charge : -879.2195 centred at (gu) : 90.26646 90.99406 90.37504 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9813 nv = 96 ne = 84 npr = 117776 no. pairs analyzed = 117776 no. exposed pairs = 7285 no. arc points = 50360 no. surface atoms = 2447 nbur = 3382 mkacc time = 0.2500000 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 = 1.680000 m= 359 mr = 5064 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2799999 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.5700000 number of dielectric boundary points 5098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4992 ## 705 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4309011E-11 -3.5492292E-10 midg,1,midg; midg,igrid,midg -1.5140107E-10 -4.4023740E-11 1,midg,midg; igrid,midg,midg -2.2647575E-10 1.4094065E-11 gauss-seidel spectral radius is 0.9807127 estimated iterations to convergence 59 setup time was (sec) 0.8000000 now iterating at: 08:24:00 rms-change max change #iterations 7.9119407E-02 12.02538 at 10iterations 4.8215981E-03 0.7152710 at 20iterations 5.2826823E-04 0.1230125 at 30iterations 1.4105617E-04 3.3866882E-02 at 40iterations 4.4741329E-05 1.0028839E-02 at 50iterations finished qdiffx linear iterations at : 08:24:02 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 4.4741329E-05 1.0028839E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 08:24:03 3.566u 0.184s 0:04.10 91.2% 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 Sun Oct 9 2011 at 08:24:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.541726 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 1.541726 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.999940 assigned positive charge : 872.2128 centred at (gu) : 90.90280 93.04653 90.95265 assigned negative charge : -879.2195 centred at (gu) : 90.79926 92.98209 91.12436 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 110494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32528 mr = 75902 m= 2824 mr = 21506 m= 57 mr = 1205 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1790 time to turn everything in is 0.7600000 number of dielectric boundary points 47290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 637 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 42564 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) : 0.5139087 object centre at (A) : 31.98450 3.012501 59.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3189973E-03 -1.3147393E-02 midg,1,midg; midg,igrid,midg -2.1233939E-02 -6.4329836E-03 1,midg,midg; igrid,midg,midg -6.9854609E-03 -7.2117946E-03 gauss-seidel spectral radius is 0.9982387 estimated iterations to convergence 189 setup time was (sec) 1.060000 now iterating at: 08:24:04 rms-change max change #iterations 4.326507 177.9849 at 10iterations 1.831984 53.89614 at 20iterations 0.7724978 22.78181 at 30iterations 0.3284204 9.170433 at 40iterations 0.1386221 3.818608 at 50iterations 5.8683176E-02 1.709854 at 60iterations 2.4880264E-02 0.7208519 at 70iterations 1.0596346E-02 0.3314518 at 80iterations 4.5034182E-03 0.1276779 at 90iterations 1.9418802E-03 5.7716370E-02 at 100iterations 8.4152678E-04 2.6138306E-02 at 110iterations 3.7700715E-04 1.3088226E-02 at 120iterations finished qdiffx linear iterations at : 08:24:11 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.7700715E-04 1.3088226E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:24:11 7.877u 0.216s 0:08.38 96.4% 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 Sun Oct 9 2011 at 08:24:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.312589 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 2.312589 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.999940 assigned positive charge : 872.2128 centred at (gu) : 91.35370 94.56962 91.42867 assigned negative charge : -879.2195 centred at (gu) : 91.19878 94.47311 91.68661 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 256955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 116083 mr = 186250 m= 29495 mr = 90211 m= 4077 mr = 21249 m= 208 mr = 2481 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 5988 time to turn everything in is 1.800000 number of dielectric boundary points 106563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 45161 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) : 1.541726 object centre at (A) : 31.98450 3.012501 59.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1292042 -0.2934724 midg,1,midg; midg,igrid,midg -0.4656875 -0.3004459 1,midg,midg; igrid,midg,midg 0.1130915 -8.2044944E-02 gauss-seidel spectral radius is 0.9992314 estimated iterations to convergence 285 setup time was (sec) 2.140000 now iterating at: 08:24:14 rms-change max change #iterations 11.77773 288.9226 at 10iterations 6.991839 150.4537 at 20iterations 4.119810 91.36461 at 30iterations 2.415884 46.88321 at 40iterations 1.410266 27.64705 at 50iterations 0.8196000 15.06028 at 60iterations 0.4760424 8.721304 at 70iterations 0.2747507 4.729610 at 80iterations 0.1584408 2.805702 at 90iterations 9.1294445E-02 1.759063 at 100iterations 5.2534048E-02 0.8779144 at 110iterations 3.0169414E-02 0.5147133 at 120iterations 1.7313141E-02 0.2762928 at 130iterations 9.9466676E-03 0.1993713 at 140iterations 5.7107131E-03 9.6059799E-02 at 150iterations 3.2767677E-03 5.6591034E-02 at 160iterations 1.8858424E-03 3.1707764E-02 at 170iterations 1.0894584E-03 1.8867493E-02 at 180iterations finished qdiffx linear iterations at : 08:24:25 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 1.0894584E-03 1.8867493E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:24:25 13.312u 0.230s 0:13.81 98.0% 0+0k 0+0io 0pf+0w