Mon Oct 10 11:51:22 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 Mon Oct 10 2011 at 11:51:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7485754 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 0.7485754 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 88.93369 90.50470 90.14310 assigned negative charge : -320.7320 centred at (gu) : 88.93206 90.57703 90.27720 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8089 nv = 96 ne = 84 npr = 43988 no. pairs analyzed = 43988 no. exposed pairs = 2682 no. arc points = 18767 no. surface atoms = 905 nbur = 1202 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4492 m= 7 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1504 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7940404E-08 -2.8220040E-07 midg,1,midg; midg,igrid,midg -2.2204773E-08 -2.1799495E-07 1,midg,midg; igrid,midg,midg -1.3632614E-07 -8.9980063E-08 gauss-seidel spectral radius is 0.9906982 estimated iterations to convergence 84 setup time was (sec) 0.5900000 now iterating at: 11:51:24 rms-change max change #iterations 0.2538191 36.08908 at 10iterations 3.5008881E-02 4.321655 at 20iterations 4.7639855E-03 0.6161854 at 30iterations 6.6586590E-04 8.4226608E-02 at 40iterations 9.2024464E-05 1.2374878E-02 at 50iterations finished qdiffx linear iterations at : 11:51:27 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 9.2024464E-05 1.2374878E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 11:51:28 4.227u 0.264s 0:04.95 90.5% 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 Mon Oct 10 2011 at 11:51:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.245726 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 2.245726 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 86.80109 91.51408 90.42950 assigned negative charge : -320.7320 centred at (gu) : 86.79621 91.73134 90.83154 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18767 grid for indexing accessible points = 1.400000 m= 33996 mr = 58410 m= 7401 mr = 25789 m= 874 mr = 5136 m= 27 mr = 497 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 37156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15686 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) : 0.7485754 object centre at (A) : 1.693500 13.86500 20.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4216052E-03 -0.1181278 midg,1,midg; midg,igrid,midg -2.4766332E-02 -3.8047161E-02 1,midg,midg; igrid,midg,midg -2.1366630E-02 -1.0656141E-02 gauss-seidel spectral radius is 0.9989455 estimated iterations to convergence 244 setup time was (sec) 0.9800000 now iterating at: 11:51:29 rms-change max change #iterations 5.192842 222.0727 at 10iterations 2.647373 80.90088 at 20iterations 1.357100 51.98317 at 30iterations 0.6961956 21.63095 at 40iterations 0.3565011 9.243973 at 50iterations 0.1834308 5.298812 at 60iterations 9.3946569E-02 2.714207 at 70iterations 4.7935456E-02 1.399179 at 80iterations 2.4697350E-02 0.6937675 at 90iterations 1.2658166E-02 0.3677597 at 100iterations 6.4963060E-03 0.1876523 at 110iterations 3.3274801E-03 9.3286514E-02 at 120iterations finished qdiffx linear iterations at : 11:51:38 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 3.3274801E-03 9.3286514E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 11:51:38 9.724u 0.284s 0:10.29 97.1% 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 11:51:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.368589 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 3.368589 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 85.20138 92.27110 90.64420 assigned negative charge : -320.7320 centred at (gu) : 85.19428 92.59702 91.24731 start vw surface at 0.1400000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 194924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18767 grid for indexing accessible points = 1.400000 m= 103741 mr = 140671 m= 44565 mr = 85875 m= 14217 mr = 36808 m= 3388 mr = 11339 m= 479 mr = 2635 m= 33 mr = 319 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.150000 number of dielectric boundary points 83679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15752 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) : 2.245726 object centre at (A) : 1.693500 13.86500 20.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6339987E-02 -1.137299 midg,1,midg; midg,igrid,midg -0.2273572 -0.1752558 1,midg,midg; igrid,midg,midg -0.2269000 -0.2138484 gauss-seidel spectral radius is 0.9993249 estimated iterations to convergence 304 setup time was (sec) 2.490000 now iterating at: 11:51:41 rms-change max change #iterations 11.07033 326.1309 at 10iterations 6.542328 120.7312 at 20iterations 3.861321 60.78572 at 30iterations 2.275570 34.94773 at 40iterations 1.342283 22.87312 at 50iterations 0.7906184 12.73273 at 60iterations 0.4658681 7.208725 at 70iterations 0.2739609 4.140659 at 80iterations 0.1615207 2.697189 at 90iterations 9.5092878E-02 1.541837 at 100iterations 5.5876698E-02 0.9264832 at 110iterations 3.2849334E-02 0.5088348 at 120iterations 1.9322490E-02 0.3370180 at 130iterations 1.1403990E-02 0.1791630 at 140iterations 6.7090099E-03 0.1021166 at 150iterations 3.9433562E-03 6.3133240E-02 at 160iterations 2.3205020E-03 3.6957264E-02 at 170iterations 1.3673464E-03 2.1995783E-02 at 180iterations finished qdiffx linear iterations at : 11:51:54 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 1.3673464E-03 2.1995783E-02 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 11:51:56 16.326u 0.296s 0:17.85 93.0% 0+0k 0+0io 0pf+0w