Mon Oct 10 13:56:01 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 13:56:02 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 0.5574957 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 0.5574957 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.014009 assigned positive charge : 418.7959 centred at (gu) : 88.01363 88.98302 91.80079 assigned negative charge : -416.7823 centred at (gu) : 87.84055 89.06135 91.76805 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 53137 no. pairs analyzed = 53137 no. exposed pairs = 4565 no. arc points = 33711 no. surface atoms = 1499 nbur = 1353 mkacc time = 8.9999996E-02 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 = 1.540000 m= 288 mr = 2576 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3319 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6731463E-11 8.1365098E-10 midg,1,midg; midg,igrid,midg 1.2143361E-09 -4.0821777E-10 1,midg,midg; igrid,midg,midg -2.3834705E-09 1.1169771E-09 gauss-seidel spectral radius is 0.9834238 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 13:56:02 rms-change max change #iterations 7.7370085E-02 18.37719 at 10iterations 5.3058909E-03 0.8927050 at 20iterations 3.8023721E-04 6.4773560E-02 at 30iterations 2.6304464E-05 4.3201447E-03 at 40iterations 2.1434573E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 13:56:05 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.1434573E-06 3.9672852E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 13:56:05 3.439u 0.162s 0:03.94 91.1% 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 13:56:06 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.672487 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 1.672487 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.014009 assigned positive charge : 418.7959 centred at (gu) : 84.04024 86.94823 95.40213 assigned negative charge : -416.7823 centred at (gu) : 83.52138 87.18381 95.30379 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20787 mr = 38893 m= 2516 mr = 13040 m= 81 mr = 1067 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 36477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20816 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) : 0.5574957 object centre at (A) : -46.07500 -19.60700 -41.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8051278E-03 2.5981679E-04 midg,1,midg; midg,igrid,midg 1.3685536E-02 4.0371409E-03 1,midg,midg; igrid,midg,midg -1.0032257E-02 1.8135719E-02 gauss-seidel spectral radius is 0.9982949 estimated iterations to convergence 192 setup time was (sec) 0.5400000 now iterating at: 13:56:06 rms-change max change #iterations 3.398788 165.0349 at 10iterations 1.447516 60.51085 at 20iterations 0.6193652 27.16923 at 30iterations 0.2642601 10.26835 at 40iterations 0.1124853 4.205415 at 50iterations 4.8111275E-02 2.221495 at 60iterations 2.0508796E-02 0.8072586 at 70iterations 8.7869233E-03 0.3147564 at 80iterations 3.7395139E-03 0.1284342 at 90iterations 1.6001656E-03 6.2349796E-02 at 100iterations 6.8451214E-04 2.5725603E-02 at 110iterations 2.9325721E-04 1.0857582E-02 at 120iterations finished qdiffx linear iterations at : 13:56:13 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.9325721E-04 1.0857582E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 13:56:14 7.783u 0.222s 0:08.41 95.1% 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 13:56:14 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.508730 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 2.508730 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.014009 assigned positive charge : 418.7959 centred at (gu) : 81.06026 85.42234 98.10317 assigned negative charge : -416.7823 centred at (gu) : 80.28197 85.77564 97.95553 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 152629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67895 mr = 96334 m= 21707 mr = 49971 m= 3740 mr = 15413 m= 288 mr = 2215 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 82241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21592 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) : 1.672487 object centre at (A) : -46.07500 -19.60700 -41.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3868938E-02 2.3692138E-02 midg,1,midg; midg,igrid,midg 0.1122457 3.5245910E-02 1,midg,midg; igrid,midg,midg -9.2678584E-02 0.3147722 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.090000 now iterating at: 13:56:15 rms-change max change #iterations 9.062829 303.0167 at 10iterations 5.292394 180.4970 at 20iterations 3.044418 93.91560 at 30iterations 1.742579 50.36411 at 40iterations 0.9924074 26.53145 at 50iterations 0.5636329 12.50054 at 60iterations 0.3182563 10.19618 at 70iterations 0.1791898 4.338167 at 80iterations 0.1011028 2.449878 at 90iterations 5.6600522E-02 1.363953 at 100iterations 3.1875413E-02 0.7565687 at 110iterations 1.7843684E-02 0.3866119 at 120iterations 1.0008410E-02 0.2517171 at 130iterations 5.6043705E-03 0.1352406 at 140iterations 3.1376085E-03 6.7966461E-02 at 150iterations 1.7543620E-03 3.8736165E-02 at 160iterations 9.8333112E-04 2.3839235E-02 at 170iterations 5.5028859E-04 1.2248039E-02 at 180iterations finished qdiffx linear iterations at : 13:56:27 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 5.5028859E-04 1.2248039E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 13:56:27 12.688u 0.192s 0:13.23 97.2% 0+0k 0+0io 0pf+0w