Sun Oct 9 03:33:10 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 03:33:10 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4903 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4208336 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): -64.68800 -0.3890001 ymin,ymax (A): 15.93600 75.76100 zmin,zma (A): -35.43900 49.15500 x,y,z range (A): 64.29900 59.82500 84.59401 scale (grids/A): 0.4208336 object centre (A): -32.53850 45.84850 6.858000 number of atom coordinates read : 4903 total number of charged atoms : 4266 net assigned charge : 19.20601 assigned positive charge : 658.6653 centred at (gu) : 89.52596 91.68994 86.23908 assigned negative charge : -639.4639 centred at (gu) : 89.57897 91.68991 86.13763 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 4792 nv = 96 ne = 84 npr = 90198 no. pairs analyzed = 90198 no. exposed pairs = 5852 no. arc points = 42019 no. surface atoms = 1959 nbur = 2944 mkacc time = 0.2000000 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 = 1.988000 m= 132 mr = 2210 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 2714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3215 ## 702 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2606139E-13 1.3621411E-12 midg,1,midg; midg,igrid,midg 1.3017367E-12 3.6933763E-12 1,midg,midg; igrid,midg,midg 3.8376051E-12 8.9990960E-13 gauss-seidel spectral radius is 0.9712299 estimated iterations to convergence 49 setup time was (sec) 0.6500000 now iterating at: 03:33:11 rms-change max change #iterations 2.5468936E-02 5.147787 at 10iterations 3.5085178E-03 0.7771378 at 20iterations 1.3700690E-03 0.3140984 at 30iterations 5.4826494E-04 0.1262665 at 40iterations 2.1976352E-04 5.0687790E-02 at 50iterations finished qdiffx linear iterations at : 03:33:13 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.1976352E-04 5.0687790E-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 03:33:14 3.312u 0.167s 0:03.76 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 Sun Oct 9 2011 at 03:33:14 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4903 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.262501 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): -64.68800 -0.3890001 ymin,ymax (A): 15.93600 75.76100 zmin,zma (A): -35.43900 49.15500 x,y,z range (A): 64.29900 59.82500 84.59401 scale (grids/A): 1.262501 object centre (A): -32.53850 45.84850 6.858000 number of atom coordinates read : 4903 total number of charged atoms : 4266 net assigned charge : 19.20601 assigned positive charge : 658.6653 centred at (gu) : 88.57633 95.06840 78.71556 assigned negative charge : -639.4639 centred at (gu) : 88.73653 95.06946 78.41246 start vw surface at 0.2000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 56243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42019 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 12684 mr = 36521 m= 599 mr = 7273 m= 6 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 512 time to turn everything in is 0.4700000 number of dielectric boundary points 25619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 671 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 29050 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) : 0.4208336 object centre at (A) : -32.53850 45.84850 6.858000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4786827E-03 2.7176340E-03 midg,1,midg; midg,igrid,midg 5.0033891E-04 2.7126458E-03 1,midg,midg; igrid,midg,midg 3.5961373E-03 2.4281808E-03 gauss-seidel spectral radius is 0.9970359 estimated iterations to convergence 147 setup time was (sec) 0.7400000 now iterating at: 03:33:15 rms-change max change #iterations 2.183550 113.1364 at 10iterations 0.7150952 31.80182 at 20iterations 0.2353041 9.789059 at 30iterations 7.7933453E-02 3.478670 at 40iterations 2.5796017E-02 1.084311 at 50iterations 8.7174037E-03 0.4103012 at 60iterations 3.3171356E-03 0.1619434 at 70iterations 1.5826785E-03 8.2162857E-02 at 80iterations 9.7830966E-04 4.7012329E-02 at 90iterations 6.8603345E-04 3.1455994E-02 at 100iterations 4.9197185E-04 2.2367477E-02 at 110iterations 3.5634948E-04 1.6216278E-02 at 120iterations finished qdiffx linear iterations at : 03:33:21 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 3.5634948E-04 1.6216278E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 03:33:21 6.902u 0.200s 0:07.39 96.0% 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 Sun Oct 9 2011 at 03:33:21 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4903 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.893751 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): -64.68800 -0.3890001 ymin,ymax (A): 15.93600 75.76100 zmin,zma (A): -35.43900 49.15500 x,y,z range (A): 64.29900 59.82500 84.59401 scale (grids/A): 1.893751 object centre (A): -32.53850 45.84850 6.858000 number of atom coordinates read : 4903 total number of charged atoms : 4266 net assigned charge : 19.20601 assigned positive charge : 658.6653 centred at (gu) : 87.86399 97.60194 73.07281 assigned negative charge : -639.4639 centred at (gu) : 88.10470 97.60404 72.61874 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 131841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42019 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 49313 mr = 91226 m= 8667 mr = 35737 m= 576 mr = 5358 m= 9 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1575 time to turn everything in is 0.9700000 number of dielectric boundary points 57879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 33269 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) : 1.262501 object centre at (A) : -32.53850 45.84850 6.858000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2586609 4.6964228E-02 midg,1,midg; midg,igrid,midg 9.8428670E-03 6.8365410E-02 1,midg,midg; igrid,midg,midg 0.1055679 8.2141541E-02 gauss-seidel spectral radius is 0.9987743 estimated iterations to convergence 226 setup time was (sec) 1.250000 now iterating at: 03:33:23 rms-change max change #iterations 6.688131 228.5291 at 10iterations 3.372096 102.3130 at 20iterations 1.687632 49.82725 at 30iterations 0.8414751 23.49721 at 40iterations 0.4184157 12.03281 at 50iterations 0.2072902 6.367877 at 60iterations 0.1022022 2.955319 at 70iterations 5.0388876E-02 1.341616 at 80iterations 2.4810597E-02 0.7254715 at 90iterations 1.2248992E-02 0.3013000 at 100iterations 6.0548312E-03 0.2091370 at 110iterations 3.0181166E-03 9.1598511E-02 at 120iterations 1.5396363E-03 4.4695854E-02 at 130iterations 8.2775083E-04 2.4021149E-02 at 140iterations 4.9074332E-04 1.3916016E-02 at 150iterations 3.2524546E-04 9.3417168E-03 at 160iterations 2.3726386E-04 6.4201355E-03 at 170iterations 1.8338177E-04 4.8627853E-03 at 180iterations finished qdiffx linear iterations at : 03:33:32 total time elapsed so far: 10.59000 # loops : 180 mean,max change (kT/e) : 1.8338177E-04 4.8627853E-03 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 03:33:32 10.772u 0.230s 0:11.28 97.5% 0+0k 0+0io 0pf+0w