Tue Oct 11 01:56:47 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 01:56:47 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2663 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 0.5915292 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): 18.04000 78.22300 ymin,ymax (A): -11.62100 44.13500 zmin,zma (A): -7.658000 35.17800 x,y,z range (A): 60.18300 55.75600 42.83600 scale (grids/A): 0.5915292 object centre (A): 48.13150 16.25700 13.76000 number of atom coordinates read : 2663 total number of charged atoms : 2512 net assigned charge : 5.312024 assigned positive charge : 401.1097 centred at (gu) : 88.10682 89.76992 89.66279 assigned negative charge : -395.7985 centred at (gu) : 88.42077 89.92219 89.83123 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6154 nv = 96 ne = 84 npr = 53979 no. pairs analyzed = 53979 no. exposed pairs = 3152 no. arc points = 22455 no. surface atoms = 1068 nbur = 1595 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3434 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.4000000 number of dielectric boundary points 2968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2176 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 7626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7209198E-09 -3.1073593E-09 midg,1,midg; midg,igrid,midg 6.0884671E-09 -2.7356173E-09 1,midg,midg; igrid,midg,midg 1.5794161E-08 -4.9695710E-09 gauss-seidel spectral radius is 0.9852145 estimated iterations to convergence 67 setup time was (sec) 0.7300000 now iterating at: 01:56:48 rms-change max change #iterations 0.1062076 16.63505 at 10iterations 9.5722908E-03 1.627449 at 20iterations 1.2987474E-03 0.2837105 at 30iterations 3.0381171E-04 7.2517395E-02 at 40iterations 7.6414435E-05 1.8722534E-02 at 50iterations finished qdiffx linear iterations at : 01:56:52 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 7.6414435E-05 1.8722534E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 01:56:53 4.490u 0.423s 0:05.32 92.2% 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 Tue Oct 11 2011 at 01:56:53 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2663 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 1.774588 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): 18.04000 78.22300 ymin,ymax (A): -11.62100 44.13500 zmin,zma (A): -7.658000 35.17800 x,y,z range (A): 60.18300 55.75600 42.83600 scale (grids/A): 1.774588 object centre (A): 48.13150 16.25700 13.76000 number of atom coordinates read : 2663 total number of charged atoms : 2512 net assigned charge : 5.312024 assigned positive charge : 401.1097 centred at (gu) : 84.31981 89.30939 88.98792 assigned negative charge : -395.7985 centred at (gu) : 85.26196 89.76620 89.49347 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22455 grid for indexing accessible points = 1.400000 m= 22341 mr = 46843 m= 3018 mr = 16428 m= 103 mr = 1842 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3840 time to turn everything in is 0.6800000 number of dielectric boundary points 27420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19625 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) : 0.5915292 object centre at (A) : 48.13150 16.25700 13.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2452930E-02 9.9528942E-04 midg,1,midg; midg,igrid,midg 2.5272606E-02 -2.3483252E-02 1,midg,midg; igrid,midg,midg 7.9006217E-03 -2.1670485E-02 gauss-seidel spectral radius is 0.9984319 estimated iterations to convergence 200 setup time was (sec) 0.9900000 now iterating at: 01:56:54 rms-change max change #iterations 3.721774 161.3640 at 10iterations 1.648912 63.82671 at 20iterations 0.7320434 28.32069 at 30iterations 0.3245260 11.48799 at 40iterations 0.1438249 4.902763 at 50iterations 6.4048484E-02 2.199734 at 60iterations 2.8587341E-02 0.9472961 at 70iterations 1.2834715E-02 0.4541626 at 80iterations 5.8228611E-03 0.1966038 at 90iterations 2.7094758E-03 0.1066742 at 100iterations 1.3228906E-03 5.5713654E-02 at 110iterations 6.9064315E-04 3.1185150E-02 at 120iterations finished qdiffx linear iterations at : 01:57:03 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 6.9064315E-04 3.1185150E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.01000 DelPhi exited at 01:57:04 10.010u 0.481s 0:11.17 93.9% 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 Tue Oct 11 2011 at 01:57:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2663 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 2.661881 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): 18.04000 78.22300 ymin,ymax (A): -11.62100 44.13500 zmin,zma (A): -7.658000 35.17800 x,y,z range (A): 60.18300 55.75600 42.83600 scale (grids/A): 2.661881 object centre (A): 48.13150 16.25700 13.76000 number of atom coordinates read : 2663 total number of charged atoms : 2512 net assigned charge : 5.312024 assigned positive charge : 401.1097 centred at (gu) : 81.47955 88.96407 88.48172 assigned negative charge : -395.7985 centred at (gu) : 82.89286 89.64929 89.24017 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 155746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22455 grid for indexing accessible points = 1.400000 m= 75249 mr = 113958 m= 24383 mr = 61584 m= 5169 mr = 19512 m= 539 mr = 3894 m= 11 mr = 348 m= 0 mr = 4 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 13036 time to turn everything in is 1.970000 number of dielectric boundary points 61797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 20089 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) : 1.774588 object centre at (A) : 48.13150 16.25700 13.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2392998 2.2733470E-02 midg,1,midg; midg,igrid,midg 0.3287505 -0.4818290 1,midg,midg; igrid,midg,midg -4.9546831E-03 -0.1318192 gauss-seidel spectral radius is 0.9991993 estimated iterations to convergence 279 setup time was (sec) 2.320000 now iterating at: 01:57:07 rms-change max change #iterations 8.929961 268.0342 at 10iterations 5.062165 117.8673 at 20iterations 2.844980 70.11514 at 30iterations 1.600290 30.91386 at 40iterations 0.8997353 17.31276 at 50iterations 0.5052308 10.08897 at 60iterations 0.2833948 5.500460 at 70iterations 0.1590655 3.101293 at 80iterations 8.9295827E-02 1.688128 at 90iterations 5.0319511E-02 0.9480501 at 100iterations 2.8294161E-02 0.5346451 at 110iterations 1.6014958E-02 0.3318596 at 120iterations 9.1142040E-03 0.1907063 at 130iterations 5.2152937E-03 0.1078072 at 140iterations 3.0456125E-03 8.1296921E-02 at 150iterations 1.8420253E-03 4.6615601E-02 at 160iterations 1.1635387E-03 2.9411316E-02 at 170iterations 7.7259896E-04 2.1270752E-02 at 180iterations finished qdiffx linear iterations at : 01:57:21 total time elapsed so far: 16.91000 # loops : 180 mean,max change (kT/e) : 7.7259896E-04 2.1270752E-02 energy calculations done at 16.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.12000 DelPhi exited at 01:57:22 17.127u 0.501s 0:17.93 98.2% 0+0k 0+0io 0pf+0w