Mon Oct 10 17:05:04 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 17:05:05 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5647566 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 0.5647566 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5140209 assigned positive charge : 453.0749 centred at (gu) : 90.72029 90.27818 89.62367 assigned negative charge : -452.5621 centred at (gu) : 90.72395 90.11511 89.51549 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6210 nv = 96 ne = 84 npr = 60398 no. pairs analyzed = 60398 no. exposed pairs = 3791 no. arc points = 26887 no. surface atoms = 1276 nbur = 1707 mkacc time = 0.1500000 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 = 1.512000 m= 237 mr = 3183 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3400000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2762 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5297804E-09 1.3613664E-09 midg,1,midg; midg,igrid,midg -2.0100761E-09 2.3546367E-09 1,midg,midg; igrid,midg,midg 9.8069115E-11 2.1777326E-11 gauss-seidel spectral radius is 0.9838268 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 17:05:06 rms-change max change #iterations 8.6499177E-02 14.95140 at 10iterations 6.2890979E-03 1.126488 at 20iterations 4.6214432E-04 7.0006371E-02 at 30iterations 3.5086188E-05 5.3396225E-03 at 40iterations 2.9889036E-06 5.6552887E-04 at 50iterations finished qdiffx linear iterations at : 17:05:09 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 2.9889036E-06 5.6552887E-04 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 17:05:11 4.502u 0.368s 0:06.82 71.2% 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 Mon Oct 10 2011 at 17:05:11 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.694270 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 1.694270 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5140209 assigned positive charge : 453.0749 centred at (gu) : 92.16029 90.83356 88.87054 assigned negative charge : -452.5621 centred at (gu) : 92.17152 90.34510 88.54614 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 20836 mr = 46562 m= 2177 mr = 14154 m= 61 mr = 1067 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 0.6100000 number of dielectric boundary points 30035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 314 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21991 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) : 0.5647566 object centre at (A) : 1.015000 2.870500 16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1420098E-03 3.9153518E-03 midg,1,midg; midg,igrid,midg -1.8228758E-02 1.3967436E-02 1,midg,midg; igrid,midg,midg 4.2283349E-03 1.8102363E-02 gauss-seidel spectral radius is 0.9983183 estimated iterations to convergence 194 setup time was (sec) 0.8900000 now iterating at: 17:05:13 rms-change max change #iterations 3.678357 168.9081 at 10iterations 1.581850 56.07461 at 20iterations 0.6785238 26.86277 at 30iterations 0.2932782 9.875212 at 40iterations 0.1261456 4.619629 at 50iterations 5.4437816E-02 1.892063 at 60iterations 2.3361899E-02 0.8413973 at 70iterations 1.0084918E-02 0.3636570 at 80iterations 4.3351403E-03 0.1525249 at 90iterations 1.8780344E-03 6.3313484E-02 at 100iterations 8.0554921E-04 2.9154778E-02 at 110iterations 3.4725765E-04 1.2634277E-02 at 120iterations finished qdiffx linear iterations at : 17:05:22 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 3.4725765E-04 1.2634277E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.36000 DelPhi exited at 17:05:23 10.368u 0.449s 0:11.73 92.0% 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 17:05:23 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.541405 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): -30.50300 32.53300 ymin,ymax (A): -20.61000 26.35100 zmin,zma (A): -7.363000 40.68400 x,y,z range (A): 63.03600 46.96100 48.04700 scale (grids/A): 2.541405 object centre (A): 1.015000 2.870500 16.66050 number of atom coordinates read : 2983 total number of charged atoms : 2843 net assigned charge : 0.5140209 assigned positive charge : 453.0749 centred at (gu) : 93.24015 91.25020 88.30571 assigned negative charge : -452.5621 centred at (gu) : 93.25710 90.51756 87.81897 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 159623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 72190 mr = 113657 m= 20310 mr = 57183 m= 3358 mr = 14961 m= 270 mr = 2200 m= 3 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 3388 time to turn everything in is 1.350000 number of dielectric boundary points 67602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22728 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) : 1.694270 object centre at (A) : 1.015000 2.870500 16.66050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9763717E-02 5.0743386E-02 midg,1,midg; midg,igrid,midg -0.2162859 0.2078867 1,midg,midg; igrid,midg,midg 0.2126590 0.3442023 gauss-seidel spectral radius is 0.9991825 estimated iterations to convergence 276 setup time was (sec) 1.690000 now iterating at: 17:05:25 rms-change max change #iterations 9.293833 299.9459 at 10iterations 5.279561 119.2910 at 20iterations 2.982195 77.41435 at 30iterations 1.681918 35.25593 at 40iterations 0.9450706 23.88790 at 50iterations 0.5294021 11.48603 at 60iterations 0.2972210 6.333221 at 70iterations 0.1660702 3.461876 at 80iterations 9.2965990E-02 1.906467 at 90iterations 5.2032460E-02 1.012153 at 100iterations 2.9016992E-02 0.5896606 at 110iterations 1.6195847E-02 0.3114138 at 120iterations 9.0344800E-03 0.1712265 at 130iterations 5.0439951E-03 0.1021900 at 140iterations 2.8150619E-03 5.7254791E-02 at 150iterations 1.5693111E-03 3.0094147E-02 at 160iterations 8.7571540E-04 1.7164230E-02 at 170iterations 4.8864703E-04 9.5748901E-03 at 180iterations finished qdiffx linear iterations at : 17:05:41 total time elapsed so far: 17.37000 # loops : 180 mean,max change (kT/e) : 4.8864703E-04 9.5748901E-03 energy calculations done at 17.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.54000 DelPhi exited at 17:05:41 17.541u 0.456s 0:18.29 98.3% 0+0k 0+0io 0pf+0w