Thu Jan 19 13:32:27 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:31 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4308832 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 0.4308832 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1028.806 centred at (gu) : 88.66183 90.32447 89.58277 assigned negative charge : -1025.615 centred at (gu) : 88.66554 90.36703 89.56044 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7365 nv = 96 ne = 84 npr = 136227 no. pairs analyzed = 136227 no. exposed pairs = 8917 no. arc points = 60247 no. surface atoms = 3006 nbur = 3764 mkacc time = 0.2300000 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 = 1.932000 m= 210 mr = 3428 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5015 ## 1050 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9063723E-13 1.8916845E-12 midg,1,midg; midg,igrid,midg 3.1332183E-12 -2.3481896E-12 1,midg,midg; igrid,midg,midg 1.4097375E-12 3.0291874E-13 gauss-seidel spectral radius is 0.9726666 estimated iterations to convergence 50 setup time was (sec) 0.6000000 now iterating at: 13:32:35 rms-change max change #iterations 3.1321317E-02 5.614042 at 10iterations 2.1010325E-03 0.3927536 at 20iterations 7.8806735E-04 0.1535873 at 30iterations 3.3806424E-04 6.5595627E-02 at 40iterations 1.4498625E-04 2.7900696E-02 at 50iterations finished qdiffx linear iterations at : 13:32:44 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.4498625E-04 2.7900696E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 13:32:45 3.790u 0.199s 0:15.08 26.3% 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 Thu Jan 19 2012 at 13:32:47 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.292650 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 1.292650 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1028.806 centred at (gu) : 85.98347 90.97131 88.74637 assigned negative charge : -1025.615 centred at (gu) : 85.99596 91.10062 88.68124 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 85764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 19995 mr = 55819 m= 1015 mr = 11770 m= 12 mr = 214 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 601 time to turn everything in is 0.4700000 number of dielectric boundary points 38983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1095 ## 34 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45805 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) : 0.4308832 object centre at (A) : 36.71250 36.63800 201.8150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7008323E-04 9.2678478E-05 midg,1,midg; midg,igrid,midg 2.6305299E-03 7.1241334E-04 1,midg,midg; igrid,midg,midg 2.0405201E-03 3.0678320E-03 gauss-seidel spectral radius is 0.9974150 estimated iterations to convergence 157 setup time was (sec) 0.6900000 now iterating at: 13:32:52 rms-change max change #iterations 3.076584 134.2201 at 10iterations 1.086365 43.36574 at 20iterations 0.3824655 12.86276 at 30iterations 0.1351342 5.470768 at 40iterations 4.7933988E-02 1.585799 at 50iterations 1.7094368E-02 0.6093483 at 60iterations 6.3689849E-03 0.2338409 at 70iterations 2.6896554E-03 0.1204796 at 80iterations 1.4359641E-03 6.0565472E-02 at 90iterations 9.4034011E-04 3.8892746E-02 at 100iterations 6.7037385E-04 2.6768684E-02 at 110iterations 4.8905978E-04 1.9329071E-02 at 120iterations finished qdiffx linear iterations at : 13:33:17 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 4.8905978E-04 1.9329071E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:33:19 8.135u 0.206s 0:31.62 26.3% 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 Thu Jan 19 2012 at 13:33:21 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6770 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.938974 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): -4.598000 78.02300 ymin,ymax (A): -1.041000 74.31700 zmin,zma (A): 167.0470 236.5830 x,y,z range (A): 82.62100 75.35800 69.53600 scale (grids/A): 1.938974 object centre (A): 36.71250 36.63800 201.8150 number of atom coordinates read : 6770 total number of charged atoms : 6607 net assigned charge : 3.200027 assigned positive charge : 1028.806 centred at (gu) : 83.97477 91.45655 88.11907 assigned negative charge : -1025.615 centred at (gu) : 83.99403 91.65098 88.02147 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 201453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 77415 mr = 140194 m= 13971 mr = 56509 m= 998 mr = 8735 m= 23 mr = 383 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 2035 time to turn everything in is 1.040000 number of dielectric boundary points 88039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 52168 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) : 1.292650 object centre at (A) : 36.71250 36.63800 201.8150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9495901E-02 -5.3355792E-03 midg,1,midg; midg,igrid,midg 4.4892386E-02 6.8193167E-02 1,midg,midg; igrid,midg,midg 0.1791595 0.1593675 gauss-seidel spectral radius is 0.9989850 estimated iterations to convergence 248 setup time was (sec) 1.310000 now iterating at: 13:33:28 rms-change max change #iterations 9.467588 250.2901 at 10iterations 5.148840 132.3387 at 20iterations 2.773688 69.80846 at 30iterations 1.484684 38.31038 at 40iterations 0.7890626 19.12418 at 50iterations 0.4191487 9.790478 at 60iterations 0.2214653 5.457354 at 70iterations 0.1167836 2.733622 at 80iterations 6.1603285E-02 1.277184 at 90iterations 3.2468975E-02 0.6708794 at 100iterations 1.7065179E-02 0.3718512 at 110iterations 8.9513855E-03 0.1977482 at 120iterations 4.7220872E-03 9.6660614E-02 at 130iterations 2.4865079E-03 5.6020021E-02 at 140iterations 1.3244498E-03 2.6636124E-02 at 150iterations 7.1709661E-04 1.4852524E-02 at 160iterations 4.0339731E-04 9.0212822E-03 at 170iterations 2.4078497E-04 6.2236786E-03 at 180iterations finished qdiffx linear iterations at : 13:34:05 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 2.4078497E-04 6.2236786E-03 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 13:34:06 13.571u 0.206s 0:44.94 30.6% 0+0k 0+0io 0pf+0w