Sun Oct 9 17:36:58 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 Sun Oct 9 2011 at 17:36:58 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5733612 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): -11.08000 51.01000 ymin,ymax (A): -12.03900 40.78100 zmin,zma (A): 19.77200 76.12600 x,y,z range (A): 62.09000 52.82000 56.35400 scale (grids/A): 0.5733612 object centre (A): 19.96500 14.37100 47.94900 number of atom coordinates read : 3142 total number of charged atoms : 3007 net assigned charge : 2.621018 assigned positive charge : 488.3761 centred at (gu) : 90.61356 89.63503 87.66082 assigned negative charge : -485.7561 centred at (gu) : 90.51072 89.73520 87.58985 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6938 nv = 96 ne = 84 npr = 60546 no. pairs analyzed = 60546 no. exposed pairs = 4296 no. arc points = 30661 no. surface atoms = 1418 nbur = 1724 mkacc time = 9.9999994E-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 = 1.484000 m= 334 mr = 3445 m= 0 mr = 17 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2956 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6193026E-09 1.0469788E-09 midg,1,midg; midg,igrid,midg 2.5740536E-09 -1.3455276E-09 1,midg,midg; igrid,midg,midg -1.3117200E-09 2.7900344E-09 gauss-seidel spectral radius is 0.9843211 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 17:36:59 rms-change max change #iterations 9.5559299E-02 15.68426 at 10iterations 7.1698250E-03 1.226434 at 20iterations 5.6032551E-04 8.5763931E-02 at 30iterations 4.6309793E-05 8.7203979E-03 at 40iterations 6.5125801E-06 1.0414124E-03 at 50iterations finished qdiffx linear iterations at : 17:37:02 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.5125801E-06 1.0414124E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:37:02 3.391u 0.177s 0:03.83 92.9% 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 Sun Oct 9 2011 at 17:37:02 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.720084 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): -11.08000 51.01000 ymin,ymax (A): -12.03900 40.78100 zmin,zma (A): 19.77200 76.12600 x,y,z range (A): 62.09000 52.82000 56.35400 scale (grids/A): 1.720084 object centre (A): 19.96500 14.37100 47.94900 number of atom coordinates read : 3142 total number of charged atoms : 3007 net assigned charge : 2.621018 assigned positive charge : 488.3761 centred at (gu) : 91.83994 88.90453 82.98166 assigned negative charge : -485.7561 centred at (gu) : 91.53166 89.20526 82.76925 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30661 grid for indexing accessible points = 1.400000 m= 25165 mr = 49957 m= 3137 mr = 16937 m= 121 mr = 1544 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 35251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23272 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) : 0.5733612 object centre at (A) : 19.96500 14.37100 47.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3195173E-03 5.3217565E-03 midg,1,midg; midg,igrid,midg 1.7251972E-02 -1.0624992E-02 1,midg,midg; igrid,midg,midg -8.3501143E-03 1.9874163E-02 gauss-seidel spectral radius is 0.9983934 estimated iterations to convergence 198 setup time was (sec) 0.5800000 now iterating at: 17:37:03 rms-change max change #iterations 3.970048 189.4490 at 10iterations 1.742939 62.03612 at 20iterations 0.7700505 29.85501 at 30iterations 0.3390231 11.58151 at 40iterations 0.1490713 5.094863 at 50iterations 6.5705940E-02 2.400879 at 60iterations 2.8950533E-02 1.071159 at 70iterations 1.2797920E-02 0.4554014 at 80iterations 5.6398958E-03 0.1914344 at 90iterations 2.4933566E-03 8.4634781E-02 at 100iterations 1.1167517E-03 3.7137985E-02 at 110iterations 5.1434734E-04 1.9589424E-02 at 120iterations finished qdiffx linear iterations at : 17:37:10 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 5.1434734E-04 1.9589424E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:37:10 7.812u 0.218s 0:08.33 96.2% 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 Sun Oct 9 2011 at 17:37:10 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.580126 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): -11.08000 51.01000 ymin,ymax (A): -12.03900 40.78100 zmin,zma (A): 19.77200 76.12600 x,y,z range (A): 62.09000 52.82000 56.35400 scale (grids/A): 2.580126 object centre (A): 19.96500 14.37100 47.94900 number of atom coordinates read : 3142 total number of charged atoms : 3007 net assigned charge : 2.621018 assigned positive charge : 488.3761 centred at (gu) : 92.75974 88.35662 79.47223 assigned negative charge : -485.7561 centred at (gu) : 92.29735 88.80796 79.15382 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 174637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30661 grid for indexing accessible points = 1.400000 m= 83713 mr = 122530 m= 26963 mr = 65168 m= 5037 mr = 20015 m= 477 mr = 3225 m= 15 mr = 235 m= 0 mr = 4 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 79665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 24049 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) : 1.720084 object centre at (A) : 19.96500 14.37100 47.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9029048E-02 6.6302881E-02 midg,1,midg; midg,igrid,midg 0.2373313 -0.2097036 1,midg,midg; igrid,midg,midg 0.1038545 0.2571340 gauss-seidel spectral radius is 0.9992140 estimated iterations to convergence 282 setup time was (sec) 1.180000 now iterating at: 17:37:12 rms-change max change #iterations 10.18549 339.4045 at 10iterations 5.993268 150.1988 at 20iterations 3.470903 85.61786 at 30iterations 2.007170 46.61636 at 40iterations 1.154540 37.19394 at 50iterations 0.6604333 13.71561 at 60iterations 0.3776099 8.799932 at 70iterations 0.2152007 4.367785 at 80iterations 0.1223512 3.127901 at 90iterations 6.9585897E-02 1.378901 at 100iterations 3.9495301E-02 0.8188829 at 110iterations 2.2430923E-02 0.4369736 at 120iterations 1.2786395E-02 0.2468598 at 130iterations 7.2623813E-03 0.1454659 at 140iterations 4.1446122E-03 8.4728718E-02 at 150iterations 2.3873930E-03 4.5935392E-02 at 160iterations 1.4022475E-03 2.9848576E-02 at 170iterations 8.5793145E-04 1.8636703E-02 at 180iterations finished qdiffx linear iterations at : 17:37:23 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 8.5793145E-04 1.8636703E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 17:37:23 12.597u 0.216s 0:13.08 97.8% 0+0k 0+0io 0pf+0w