Sat Oct 8 19:32:18 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 19:32:18 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 = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7036130 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 0.7036130 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 88.41763 91.97497 90.72495 assigned negative charge : -389.1955 centred at (gu) : 88.29161 92.08407 90.65834 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8765 nv = 96 ne = 84 npr = 54749 no. pairs analyzed = 54749 no. exposed pairs = 3015 no. arc points = 21276 no. surface atoms = 1017 nbur = 1589 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 574 mr = 5128 m= 7 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 0.3200000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4502522E-09 8.2650033E-08 midg,1,midg; midg,igrid,midg 6.4836222E-08 -4.2090218E-08 1,midg,midg; igrid,midg,midg -5.2024504E-08 7.6696857E-08 gauss-seidel spectral radius is 0.9895223 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 19:32:19 rms-change max change #iterations 0.2216614 29.35434 at 10iterations 2.7360039E-02 3.435249 at 20iterations 3.3760713E-03 0.4117632 at 30iterations 4.1204001E-04 5.9774399E-02 at 40iterations 5.0680181E-05 5.9052706E-03 at 50iterations finished qdiffx linear iterations at : 19:32:23 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 5.0680181E-05 5.9052706E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 19:32:23 4.479u 0.405s 0:05.15 94.5% 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 19:32:24 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 = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.110839 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 2.110839 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 85.25257 95.92439 92.17445 assigned negative charge : -389.1955 centred at (gu) : 84.87450 96.25199 91.97480 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21276 grid for indexing accessible points = 1.400000 m= 37706 mr = 65798 m= 7798 mr = 29448 m= 785 mr = 5553 m= 27 mr = 421 m= 0 mr = 3 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 6596 time to turn everything in is 0.7600000 number of dielectric boundary points 37466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 19592 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) : 0.7036130 object centre at (A) : 19.00050 22.40800 15.94800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5783895E-02 1.9820647E-02 midg,1,midg; midg,igrid,midg -1.0446562E-03 -3.1673152E-02 1,midg,midg; igrid,midg,midg -1.0089733E-02 0.1127843 gauss-seidel spectral radius is 0.9988663 estimated iterations to convergence 235 setup time was (sec) 1.060000 now iterating at: 19:32:25 rms-change max change #iterations 5.232071 213.3500 at 10iterations 2.601227 82.50128 at 20iterations 1.302898 37.98537 at 30iterations 0.6521261 19.15538 at 40iterations 0.3278539 8.708076 at 50iterations 0.1635925 4.379934 at 60iterations 8.2120381E-02 2.336681 at 70iterations 4.1158270E-02 1.264288 at 80iterations 2.0592909E-02 0.6095810 at 90iterations 1.0360743E-02 0.2839985 at 100iterations 5.1915706E-03 0.1465225 at 110iterations 2.6031227E-03 6.8588257E-02 at 120iterations finished qdiffx linear iterations at : 19:32:35 total time elapsed so far: 10.77000 # loops : 120 mean,max change (kT/e) : 2.6031227E-03 6.8588257E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 19:32:35 10.938u 0.460s 0:11.69 97.4% 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 Sat Oct 8 2011 at 19:32:35 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 = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! 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: ZN3 392 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.166258 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): -5.763000 43.76400 ymin,ymax (A): -2.890000 47.70600 zmin,zma (A): -8.329000 40.22500 x,y,z range (A): 49.52700 50.59600 48.55400 scale (grids/A): 3.166258 object centre (A): 19.00050 22.40800 15.94800 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 82.87868 98.88640 93.26144 assigned negative charge : -389.1955 centred at (gu) : 82.31180 99.37797 92.96225 start vw surface at 0.1300000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 212598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21276 grid for indexing accessible points = 1.400000 m= 116307 mr = 157865 m= 49328 mr = 98143 m= 15208 mr = 41654 m= 3205 mr = 12299 m= 402 mr = 2475 m= 10 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 22342 time to turn everything in is 2.380000 number of dielectric boundary points 84353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 19724 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) : 2.110839 object centre at (A) : 19.00050 22.40800 15.94800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4427364 0.1457641 midg,1,midg; midg,igrid,midg -9.3245812E-02 -0.2114317 1,midg,midg; igrid,midg,midg -0.1410873 1.581861 gauss-seidel spectral radius is 0.9993129 estimated iterations to convergence 301 setup time was (sec) 2.730000 now iterating at: 19:32:38 rms-change max change #iterations 11.45561 395.9726 at 10iterations 6.745219 132.2896 at 20iterations 3.970227 75.54220 at 30iterations 2.331899 42.20929 at 40iterations 1.371012 24.03029 at 50iterations 0.8059393 12.98488 at 60iterations 0.4731443 7.483742 at 70iterations 0.2779524 4.433146 at 80iterations 0.1630210 2.559913 at 90iterations 9.5586292E-02 1.589085 at 100iterations 5.6067087E-02 0.8938656 at 110iterations 3.2913659E-02 0.5539589 at 120iterations 1.9278076E-02 0.3135641 at 130iterations 1.1317992E-02 0.1784840 at 140iterations 6.6519268E-03 0.1060240 at 150iterations 3.9001792E-03 6.4446211E-02 at 160iterations 2.2905534E-03 3.6510468E-02 at 170iterations 1.3444870E-03 2.1213531E-02 at 180iterations finished qdiffx linear iterations at : 19:32:55 total time elapsed so far: 19.19000 # loops : 180 mean,max change (kT/e) : 1.3444870E-03 2.1213531E-02 energy calculations done at 19.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.37000 DelPhi exited at 19:32:55 19.375u 0.475s 0:20.17 98.3% 0+0k 0+0io 0pf+0w