Sat Oct 8 18:32:54 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 Sat Oct 8 2011 at 18:32:54 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6216168 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 0.6216168 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.37095 89.23991 89.83663 assigned negative charge : -387.4045 centred at (gu) : 88.26091 89.27606 89.71881 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 55175 no. pairs analyzed = 55175 no. exposed pairs = 2935 no. arc points = 21127 no. surface atoms = 991 nbur = 1603 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3693 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 227 time to turn everything in is 0.3400000 number of dielectric boundary points 3096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2086 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8021 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9399906E-09 1.1161069E-08 midg,1,midg; midg,igrid,midg 7.0947248E-09 8.6988183E-10 1,midg,midg; igrid,midg,midg -6.1740679E-09 7.7410327E-09 gauss-seidel spectral radius is 0.9865907 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 18:32:55 rms-change max change #iterations 0.1297356 19.78632 at 10iterations 1.1761509E-02 1.958509 at 20iterations 1.0918134E-03 0.1587677 at 30iterations 1.0266514E-04 1.4659882E-02 at 40iterations 9.5948808E-06 1.3999939E-03 at 50iterations finished qdiffx linear iterations at : 18:32:58 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 9.5948808E-06 1.3999939E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 18:32:59 4.058u 0.275s 0:04.62 93.5% 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 Sat Oct 8 2011 at 18:32:59 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.864851 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 1.864851 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.11248 87.71936 89.50940 assigned negative charge : -387.4045 centred at (gu) : 84.78259 87.82787 89.15617 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21127 grid for indexing accessible points = 1.400000 m= 24650 mr = 49549 m= 3549 mr = 18471 m= 207 mr = 2267 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 8666 time to turn everything in is 0.6300000 number of dielectric boundary points 28523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19226 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) : 0.6216168 object centre at (A) : -7.021000 -0.3219995 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5235707E-02 3.0797046E-02 midg,1,midg; midg,igrid,midg 1.2598639E-02 2.3338643E-03 1,midg,midg; igrid,midg,midg -9.8281559E-03 3.5392936E-02 gauss-seidel spectral radius is 0.9985698 estimated iterations to convergence 210 setup time was (sec) 0.9300000 now iterating at: 18:33:00 rms-change max change #iterations 4.034512 174.0165 at 10iterations 1.852367 64.17744 at 20iterations 0.8554664 33.46400 at 30iterations 0.3917811 14.57634 at 40iterations 0.1811446 6.163351 at 50iterations 8.3271764E-02 2.824612 at 60iterations 3.8402338E-02 1.244095 at 70iterations 1.7690260E-02 0.5644989 at 80iterations 8.1231920E-03 0.2464390 at 90iterations 3.7581152E-03 0.1196060 at 100iterations 1.7223132E-03 5.4817200E-02 at 110iterations 7.9581066E-04 2.4934769E-02 at 120iterations finished qdiffx linear iterations at : 18:33:08 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 7.9581066E-04 2.4934769E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 18:33:09 9.322u 0.291s 0:09.94 96.6% 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 Sat Oct 8 2011 at 18:33:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.797276 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 2.797276 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.66850 86.57893 89.26405 assigned negative charge : -387.4045 centred at (gu) : 82.17393 86.74173 88.73431 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 163290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21127 grid for indexing accessible points = 1.400000 m= 81656 mr = 119892 m= 28044 mr = 67780 m= 6359 mr = 22716 m= 881 mr = 4873 m= 52 mr = 658 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 29294 time to turn everything in is 1.570000 number of dielectric boundary points 64331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19627 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) : 1.864851 object centre at (A) : -7.021000 -0.3219995 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0440456E-02 0.3706682 midg,1,midg; midg,igrid,midg 0.1520783 2.6824879E-02 1,midg,midg; igrid,midg,midg -8.3458193E-02 0.4597444 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.900000 now iterating at: 18:33:11 rms-change max change #iterations 9.492631 336.6620 at 10iterations 5.430970 116.7185 at 20iterations 3.096722 59.06854 at 30iterations 1.761832 36.61095 at 40iterations 1.003257 18.06244 at 50iterations 0.5705976 10.54156 at 60iterations 0.3245019 6.259871 at 70iterations 0.1845919 3.228348 at 80iterations 0.1049746 1.887231 at 90iterations 5.9587799E-02 1.172525 at 100iterations 3.3816207E-02 0.6470366 at 110iterations 1.9288013E-02 0.3596954 at 120iterations 1.0954510E-02 0.1943989 at 130iterations 6.2135658E-03 0.1177597 at 140iterations 3.5365552E-03 6.2356949E-02 at 150iterations 2.0070951E-03 3.7545204E-02 at 160iterations 1.1405540E-03 2.3056030E-02 at 170iterations 6.4849062E-04 1.1922836E-02 at 180iterations finished qdiffx linear iterations at : 18:33:25 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 6.4849062E-04 1.1922836E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 18:33:25 15.495u 0.295s 0:16.11 97.9% 0+0k 0+0io 0pf+0w