Mon Oct 10 19:33:04 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 Mon Oct 10 2011 at 19:33:04 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 239 has a net charge of 0.5140 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: 0.5947309 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): 2.395000 57.20200 ymin,ymax (A): -14.87400 44.98500 zmin,zma (A): 32.65600 88.26700 x,y,z range (A): 54.80700 59.85900 55.61100 scale (grids/A): 0.5947309 object centre (A): 29.79850 15.05550 60.46150 number of atom coordinates read : 2756 total number of charged atoms : 2617 net assigned charge : 7.528038 assigned positive charge : 410.9504 centred at (gu) : 89.62908 87.81115 92.09415 assigned negative charge : -403.4238 centred at (gu) : 89.69698 87.85786 92.08405 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6486 nv = 96 ne = 84 npr = 54906 no. pairs analyzed = 54906 no. exposed pairs = 3705 no. arc points = 26324 no. surface atoms = 1253 nbur = 1503 mkacc time = 8.9999996E-02 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 = 1.484000 m= 340 mr = 3252 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2641 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8110 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4664783E-09 4.7302482E-09 midg,1,midg; midg,igrid,midg 6.7739845E-09 7.2823314E-10 1,midg,midg; igrid,midg,midg 5.1932578E-09 4.2638912E-10 gauss-seidel spectral radius is 0.9853899 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 19:33:05 rms-change max change #iterations 0.1053352 17.31239 at 10iterations 8.6061452E-03 1.230211 at 20iterations 7.6473702E-04 0.1130981 at 30iterations 8.6103501E-05 1.5538216E-02 at 40iterations 1.6093325E-05 3.5991669E-03 at 50iterations finished qdiffx linear iterations at : 19:33:07 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.6093325E-05 3.5991669E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:33:09 3.416u 0.194s 0:05.36 67.1% 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 Mon Oct 10 2011 at 19:33:09 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 239 has a net charge of 0.5140 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: 1.784193 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): 2.395000 57.20200 ymin,ymax (A): -14.87400 44.98500 zmin,zma (A): 32.65600 88.26700 x,y,z range (A): 54.80700 59.85900 55.61100 scale (grids/A): 1.784193 object centre (A): 29.79850 15.05550 60.46150 number of atom coordinates read : 2756 total number of charged atoms : 2617 net assigned charge : 7.528038 assigned positive charge : 410.9504 centred at (gu) : 88.88642 83.43279 96.28178 assigned negative charge : -403.4238 centred at (gu) : 89.09083 83.57373 96.25214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26324 grid for indexing accessible points = 1.400000 m= 23433 mr = 46908 m= 3227 mr = 16222 m= 172 mr = 1658 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 32811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20377 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) : 0.5947309 object centre at (A) : 29.79850 15.05550 60.46150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3396942E-02 -5.0759180E-03 midg,1,midg; midg,igrid,midg 3.6339656E-02 1.2023431E-02 1,midg,midg; igrid,midg,midg 2.1187600E-02 3.1085698E-02 gauss-seidel spectral radius is 0.9984683 estimated iterations to convergence 203 setup time was (sec) 0.5600000 now iterating at: 19:33:10 rms-change max change #iterations 3.844482 177.3247 at 10iterations 1.708912 61.98549 at 20iterations 0.7617680 28.76022 at 30iterations 0.3416470 12.19814 at 40iterations 0.1520458 4.811972 at 50iterations 6.7794114E-02 2.237956 at 60iterations 3.0428812E-02 1.079084 at 70iterations 1.3585505E-02 0.5125661 at 80iterations 6.0862568E-03 0.2010345 at 90iterations 2.7248468E-03 9.0026855E-02 at 100iterations 1.2200862E-03 4.0651321E-02 at 110iterations 5.4764602E-04 1.9640923E-02 at 120iterations finished qdiffx linear iterations at : 19:33:17 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 5.4764602E-04 1.9640923E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 19:33:19 7.839u 0.217s 0:09.77 82.2% 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 Mon Oct 10 2011 at 19:33:19 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIR 113 has a net charge of 0.5140 !!! WARNING: HIR 239 has a net charge of 0.5140 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: 2.676289 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): 2.395000 57.20200 ymin,ymax (A): -14.87400 44.98500 zmin,zma (A): 32.65600 88.26700 x,y,z range (A): 54.80700 59.85900 55.61100 scale (grids/A): 2.676289 object centre (A): 29.79850 15.05550 60.46150 number of atom coordinates read : 2756 total number of charged atoms : 2617 net assigned charge : 7.528038 assigned positive charge : 410.9504 centred at (gu) : 88.32964 80.14886 99.42253 assigned negative charge : -403.4238 centred at (gu) : 88.63613 80.36051 99.37822 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26324 grid for indexing accessible points = 1.400000 m= 77736 mr = 114828 m= 25902 mr = 61171 m= 5338 mr = 19638 m= 686 mr = 3552 m= 66 mr = 403 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 74013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 20928 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) : 1.784193 object centre at (A) : 29.79850 15.05550 60.46150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2818140 -0.1921480 midg,1,midg; midg,igrid,midg 0.6864850 7.3974751E-02 1,midg,midg; igrid,midg,midg 0.1576222 0.6416879 gauss-seidel spectral radius is 0.9992255 estimated iterations to convergence 284 setup time was (sec) 1.160000 now iterating at: 19:33:21 rms-change max change #iterations 9.521454 379.9344 at 10iterations 5.589340 145.5675 at 20iterations 3.250185 67.37035 at 30iterations 1.874940 41.43585 at 40iterations 1.079935 24.11702 at 50iterations 0.6201925 13.05455 at 60iterations 0.3538186 6.896061 at 70iterations 0.2023565 4.660336 at 80iterations 0.1153122 2.160164 at 90iterations 6.5796241E-02 1.388335 at 100iterations 3.7459575E-02 0.7425690 at 110iterations 2.1282032E-02 0.4507866 at 120iterations 1.2104257E-02 0.2463198 at 130iterations 6.8910979E-03 0.1319580 at 140iterations 3.9084782E-03 7.5553894E-02 at 150iterations 2.2247934E-03 4.4418335E-02 at 160iterations 1.2671333E-03 2.5648355E-02 at 170iterations 7.2415551E-04 1.4397621E-02 at 180iterations finished qdiffx linear iterations at : 19:33:33 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 7.2415551E-04 1.4397621E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 19:33:35 13.262u 0.251s 0:15.35 88.0% 0+0k 0+0io 0pf+0w