Wed Dec 21 14:21:43 PST 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 Wed Dec 21 2011 at 14:21:44 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6053187 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 0.6053187 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1816 net assigned charge : 2.681005 assigned positive charge : 284.1861 centred at (gu) : 91.08957 90.30943 89.78864 assigned negative charge : -281.5053 centred at (gu) : 91.21870 90.44497 89.79504 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4700 nv = 96 ne = 84 npr = 40818 no. pairs analyzed = 40818 no. exposed pairs = 2397 no. arc points = 16986 no. surface atoms = 821 nbur = 1128 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 215 mr = 2507 m= 1 mr = 16 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 0.2800000 number of dielectric boundary points 2393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 5767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7084786E-09 1.1774109E-09 midg,1,midg; midg,igrid,midg 5.2080558E-09 -3.0688965E-09 1,midg,midg; igrid,midg,midg 4.2202348E-09 -3.4289220E-09 gauss-seidel spectral radius is 0.9858158 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 14:21:45 rms-change max change #iterations 9.5485270E-02 18.13377 at 10iterations 8.2312599E-03 1.475108 at 20iterations 7.0049334E-04 0.1247253 at 30iterations 6.0126527E-05 1.1418819E-02 at 40iterations 5.3078516E-06 8.6975098E-04 at 50iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 4.680000 # loops : 50 mean,max change (kT/e) : 5.3078516E-06 8.6975098E-04 energy calculations done at 4.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 14:21:53 4.884u 0.312s 0:10.36 50.0% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:56 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.815956 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 1.815956 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1816 net assigned charge : 2.681005 assigned positive charge : 284.1861 centred at (gu) : 93.26868 90.92825 89.36580 assigned negative charge : -281.5053 centred at (gu) : 93.65625 91.33514 89.38538 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 50654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 17311 mr = 34302 m= 2239 mr = 12637 m= 92 mr = 1281 m= 0 mr = 36 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 681 time to turn everything in is 0.4600000 number of dielectric boundary points 22040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14192 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) : 0.6053187 object centre at (A) : 28.91500 5.458500 18.34200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3159398E-02 2.5268707E-02 midg,1,midg; midg,igrid,midg 8.3180293E-03 -1.0702664E-03 1,midg,midg; igrid,midg,midg 5.7627782E-03 -1.8598610E-03 gauss-seidel spectral radius is 0.9984171 estimated iterations to convergence 199 setup time was (sec) 0.7700000 now iterating at: 14:21:58 rms-change max change #iterations 3.213790 166.0767 at 10iterations 1.413505 55.13525 at 20iterations 0.6269374 24.92499 at 30iterations 0.2766822 10.12992 at 40iterations 0.1218070 4.631944 at 50iterations 5.3652339E-02 2.176950 at 60iterations 2.3752544E-02 0.9429474 at 70iterations 1.0526890E-02 0.4543533 at 80iterations 4.6397289E-03 0.1789036 at 90iterations 2.0486647E-03 8.0223083E-02 at 100iterations 9.0368814E-04 3.2701492E-02 at 110iterations 4.0025843E-04 1.6984940E-02 at 120iterations finished qdiffx linear iterations at : 14:22:09 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 4.0025843E-04 1.6984940E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 14:22:14 11.544u 0.317s 0:18.31 64.7% 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 Wed Dec 21 2011 at 14:22:15 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1949 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.723934 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): 8.765000 49.06500 ymin,ymax (A): -15.46600 26.38300 zmin,zma (A): -11.06400 47.74800 x,y,z range (A): 40.30000 41.84900 58.81200 scale (grids/A): 2.723934 object centre (A): 28.91500 5.458500 18.34200 number of atom coordinates read : 1949 total number of charged atoms : 1816 net assigned charge : 2.681005 assigned positive charge : 284.1861 centred at (gu) : 94.90302 91.39252 89.04880 assigned negative charge : -281.5053 centred at (gu) : 95.48444 92.00282 89.07819 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 117191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16986 grid for indexing accessible points = 1.400000 m= 56824 mr = 83106 m= 18978 mr = 46268 m= 3925 mr = 15212 m= 483 mr = 2907 m= 18 mr = 292 m= 0 mr = 9 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 1.170000 number of dielectric boundary points 49625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14523 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) : 1.815956 object centre at (A) : 28.91500 5.458500 18.34200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2958077 0.2411517 midg,1,midg; midg,igrid,midg 6.5810785E-02 3.6132146E-02 1,midg,midg; igrid,midg,midg 3.8213734E-02 1.9403387E-02 gauss-seidel spectral radius is 0.9991787 estimated iterations to convergence 276 setup time was (sec) 1.490000 now iterating at: 14:22:17 rms-change max change #iterations 7.735075 312.8679 at 10iterations 4.345434 113.4609 at 20iterations 2.442684 54.49936 at 30iterations 1.363205 31.39988 at 40iterations 0.7593406 18.65550 at 50iterations 0.4230301 9.814831 at 60iterations 0.2354954 5.495689 at 70iterations 0.1308313 3.062368 at 80iterations 7.3017493E-02 1.454597 at 90iterations 4.0503193E-02 0.9594650 at 100iterations 2.2545002E-02 0.4871674 at 110iterations 1.2554552E-02 0.2842007 at 120iterations 6.9795009E-03 0.1437511 at 130iterations 3.8849628E-03 9.6838236E-02 at 140iterations 2.1636602E-03 4.7252655E-02 at 150iterations 1.2018624E-03 2.5496483E-02 at 160iterations 6.6821906E-04 1.4374733E-02 at 170iterations 3.7218482E-04 8.3646774E-03 at 180iterations finished qdiffx linear iterations at : 14:22:35 total time elapsed so far: 19.41000 # loops : 180 mean,max change (kT/e) : 3.7218482E-04 8.3646774E-03 energy calculations done at 19.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.60000 DelPhi exited at 14:22:41 19.602u 0.326s 0:26.12 76.2% 0+0k 0+0io 0pf+0w