Tue Oct 11 06:01:03 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 Tue Oct 11 2011 at 06:01:04 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7156498 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 0.7156498 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 89.11478 90.16125 90.29670 assigned negative charge : -319.8310 centred at (gu) : 89.25352 90.09060 90.37822 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7294 nv = 96 ne = 84 npr = 42822 no. pairs analyzed = 42822 no. exposed pairs = 2558 no. arc points = 17462 no. surface atoms = 886 nbur = 1432 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4209 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1621 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8096 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0319777E-07 1.0559550E-08 midg,1,midg; midg,igrid,midg 1.6460913E-08 1.0590912E-07 1,midg,midg; igrid,midg,midg 1.6999697E-07 -2.0750555E-08 gauss-seidel spectral radius is 0.9898217 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 06:01:04 rms-change max change #iterations 0.2176282 33.42232 at 10iterations 2.7921161E-02 3.947603 at 20iterations 3.9149686E-03 0.4623337 at 30iterations 7.3687261E-04 0.1008759 at 40iterations 2.0803708E-04 2.6500702E-02 at 50iterations finished qdiffx linear iterations at : 06:01:07 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.0803708E-04 2.6500702E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:01:07 3.318u 0.181s 0:03.83 91.1% 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 Tue Oct 11 2011 at 06:01:07 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.146949 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 2.146949 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 87.34435 90.48368 90.89005 assigned negative charge : -319.8310 centred at (gu) : 87.76064 90.27177 91.13492 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17462 grid for indexing accessible points = 1.400000 m= 31773 mr = 55048 m= 6249 mr = 24295 m= 609 mr = 4247 m= 20 mr = 296 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15808 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) : 0.7156498 object centre at (A) : 49.22550 6.410501 25.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2109915E-02 3.2985270E-02 midg,1,midg; midg,igrid,midg 3.8783643E-02 3.0164652E-02 1,midg,midg; igrid,midg,midg 4.8234858E-02 -5.9906363E-02 gauss-seidel spectral radius is 0.9988557 estimated iterations to convergence 234 setup time was (sec) 0.8600000 now iterating at: 06:01:08 rms-change max change #iterations 4.787191 209.6771 at 10iterations 2.384979 81.67757 at 20iterations 1.195588 37.17709 at 30iterations 0.5966343 18.03935 at 40iterations 0.2993456 8.933455 at 50iterations 0.1490889 4.181129 at 60iterations 7.4810334E-02 2.150947 at 70iterations 3.7732769E-02 1.093614 at 80iterations 1.8940901E-02 0.5362177 at 90iterations 9.6308766E-03 0.2744312 at 100iterations 4.9173469E-03 0.1666260 at 110iterations 2.6000780E-03 7.8384399E-02 at 120iterations finished qdiffx linear iterations at : 06:01:15 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 2.6000780E-03 7.8384399E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 06:01:16 7.544u 0.233s 0:08.19 94.8% 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 Tue Oct 11 2011 at 06:01:16 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.220424 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): 25.86900 72.58200 ymin,ymax (A): -18.46200 31.28300 zmin,zma (A): 4.071000 46.48400 x,y,z range (A): 46.71300 49.74500 42.41300 scale (grids/A): 3.220424 object centre (A): 49.22550 6.410501 25.27750 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 86.01659 90.72564 91.33508 assigned negative charge : -319.8310 centred at (gu) : 86.64091 90.40775 91.70235 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 178337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17462 grid for indexing accessible points = 1.400000 m= 98452 mr = 132765 m= 41107 mr = 82332 m= 11980 mr = 33977 m= 2452 mr = 9395 m= 291 mr = 1752 m= 14 mr = 169 m= 0 mr = 5 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 72238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15904 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) : 2.146949 object centre at (A) : 49.22550 6.410501 25.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1143300 0.2500696 midg,1,midg; midg,igrid,midg 0.3165546 0.1499078 1,midg,midg; igrid,midg,midg 0.4778050 -0.6897605 gauss-seidel spectral radius is 0.9993029 estimated iterations to convergence 299 setup time was (sec) 2.160000 now iterating at: 06:01:18 rms-change max change #iterations 10.56832 360.3873 at 10iterations 6.263750 147.1292 at 20iterations 3.716439 72.16424 at 30iterations 2.201894 45.05147 at 40iterations 1.297544 24.11215 at 50iterations 0.7631370 15.02370 at 60iterations 0.4501473 7.756974 at 70iterations 0.2648173 5.143497 at 80iterations 0.1558197 2.643864 at 90iterations 9.1721743E-02 1.566109 at 100iterations 5.3977698E-02 0.8763443 at 110iterations 3.1980004E-02 0.5194321 at 120iterations 1.9112302E-02 0.3225822 at 130iterations 1.1660368E-02 0.2164268 at 140iterations 7.2882036E-03 0.1418343 at 150iterations 4.7464962E-03 0.1016998 at 160iterations 3.2780480E-03 6.6604614E-02 at 170iterations 2.3928627E-03 4.7668457E-02 at 180iterations finished qdiffx linear iterations at : 06:01:28 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 2.3928627E-03 4.7668457E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 06:01:29 12.692u 0.218s 0:13.22 97.5% 0+0k 0+0io 0pf+0w