Sun Oct 9 21:35:01 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 21:35:01 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 0.6586494 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): 45.57900 98.54700 ymin,ymax (A): 2.996000 57.04600 zmin,zma (A): 15.26700 68.16700 x,y,z range (A): 52.96800 54.05000 52.90000 scale (grids/A): 0.6586494 object centre (A): 72.06300 30.02100 41.71700 number of atom coordinates read : 3152 total number of charged atoms : 3002 net assigned charge : 7.425008 assigned positive charge : 482.0608 centred at (gu) : 90.58239 88.49717 90.61275 assigned negative charge : -474.6371 centred at (gu) : 90.50802 88.44082 90.60532 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9338 nv = 96 ne = 84 npr = 61793 no. pairs analyzed = 61793 no. exposed pairs = 4073 no. arc points = 29316 no. surface atoms = 1370 nbur = 1782 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4950 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2500000 number of dielectric boundary points 4874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2831 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 10984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4621854E-08 2.2620675E-08 midg,1,midg; midg,igrid,midg 6.5058527E-09 2.3036840E-08 1,midg,midg; igrid,midg,midg 8.0108364E-10 3.9995868E-08 gauss-seidel spectral radius is 0.9881142 estimated iterations to convergence 75 setup time was (sec) 0.4600000 now iterating at: 21:35:02 rms-change max change #iterations 0.1876106 23.01039 at 10iterations 1.9715762E-02 3.034101 at 20iterations 2.1005718E-03 0.3009033 at 30iterations 2.2071398E-04 3.2054901E-02 at 40iterations 2.4162702E-05 3.0546188E-03 at 50iterations finished qdiffx linear iterations at : 21:35:04 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 2.4162702E-05 3.0546188E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 21:35:05 3.478u 0.156s 0:03.91 92.5% 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 Sun Oct 9 2011 at 21:35:05 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 1.975948 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): 45.57900 98.54700 ymin,ymax (A): 2.996000 57.04600 zmin,zma (A): 15.26700 68.16700 x,y,z range (A): 52.96800 54.05000 52.90000 scale (grids/A): 1.975948 object centre (A): 72.06300 30.02100 41.71700 number of atom coordinates read : 3152 total number of charged atoms : 3002 net assigned charge : 7.425008 assigned positive charge : 482.0608 centred at (gu) : 91.74655 85.49081 91.83778 assigned negative charge : -474.6371 centred at (gu) : 91.52365 85.32191 91.81570 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 100277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 grid for indexing accessible points = 1.400000 m= 36442 mr = 68320 m= 6143 mr = 26373 m= 487 mr = 3757 m= 11 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2331 time to turn everything in is 0.4900000 number of dielectric boundary points 44698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 23680 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) : 0.6586494 object centre at (A) : 72.06300 30.02100 41.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9243003E-03 -1.8947851E-02 midg,1,midg; midg,igrid,midg 9.2238627E-02 5.7551168E-02 1,midg,midg; igrid,midg,midg 3.0532207E-03 3.6553189E-02 gauss-seidel spectral radius is 0.9987913 estimated iterations to convergence 228 setup time was (sec) 0.7200000 now iterating at: 21:35:06 rms-change max change #iterations 5.108427 219.1822 at 10iterations 2.501048 70.58736 at 20iterations 1.219725 37.96040 at 30iterations 0.5959236 16.10955 at 40iterations 0.2916863 8.214428 at 50iterations 0.1423542 3.902985 at 60iterations 6.9700547E-02 2.007671 at 70iterations 3.4095556E-02 0.8839064 at 80iterations 1.6657647E-02 0.4466920 at 90iterations 8.1425272E-03 0.2161026 at 100iterations 4.0039900E-03 0.1073418 at 110iterations 1.9577877E-03 5.6667805E-02 at 120iterations finished qdiffx linear iterations at : 21:35:13 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.9577877E-03 5.6667805E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 21:35:13 8.106u 0.193s 0:08.57 96.7% 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 Sun Oct 9 2011 at 21:35:13 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: HIZ 560 has a net charge of 0.2000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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: 2.963922 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): 45.57900 98.54700 ymin,ymax (A): 2.996000 57.04600 zmin,zma (A): 15.26700 68.16700 x,y,z range (A): 52.96800 54.05000 52.90000 scale (grids/A): 2.963922 object centre (A): 72.06300 30.02100 41.71700 number of atom coordinates read : 3152 total number of charged atoms : 3002 net assigned charge : 7.425008 assigned positive charge : 482.0608 centred at (gu) : 92.61963 83.23609 92.75643 assigned negative charge : -474.6371 centred at (gu) : 92.28525 82.98287 92.72349 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 231865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 grid for indexing accessible points = 1.400000 m= 116771 mr = 166001 m= 43193 mr = 94591 m= 11217 mr = 33996 m= 1896 mr = 8278 m= 167 mr = 1282 m= 5 mr = 83 m= 0 mr = 2 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 8011 time to turn everything in is 1.270000 number of dielectric boundary points 100881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 24016 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) : 1.975948 object centre at (A) : 72.06300 30.02100 41.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3538168E-02 -0.3835080 midg,1,midg; midg,igrid,midg 0.5858904 0.5069095 1,midg,midg; igrid,midg,midg 0.1732505 0.4835307 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 1.520000 now iterating at: 21:35:15 rms-change max change #iterations 11.92935 415.4207 at 10iterations 7.194861 171.9796 at 20iterations 4.310619 82.61668 at 30iterations 2.584919 45.29121 at 40iterations 1.537905 25.64408 at 50iterations 0.9145007 17.15434 at 60iterations 0.5431327 8.906683 at 70iterations 0.3218621 5.924448 at 80iterations 0.1908125 3.005758 at 90iterations 0.1124598 1.836509 at 100iterations 6.6519558E-02 1.240087 at 110iterations 3.9288063E-02 0.7050519 at 120iterations 2.3185724E-02 0.4087219 at 130iterations 1.3677779E-02 0.2248795 at 140iterations 8.0682645E-03 0.1206608 at 150iterations 4.7684186E-03 7.7025414E-02 at 160iterations 2.8159595E-03 4.5734406E-02 at 170iterations 1.6619746E-03 2.8018951E-02 at 180iterations finished qdiffx linear iterations at : 21:35:27 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.6619746E-03 2.8018951E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 21:35:28 13.595u 0.221s 0:14.09 98.0% 0+0k 0+0io 0pf+0w