Mon Oct 10 16:10:12 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+sph.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 = amb.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 16:10:12 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5563891 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): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 0.5563891 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 546.9006 centred at (gu) : 89.39173 90.20023 91.25073 assigned negative charge : -541.7030 centred at (gu) : 89.32272 90.27395 91.31490 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7569 nv = 96 ne = 84 npr = 73850 no. pairs analyzed = 73850 no. exposed pairs = 4699 no. arc points = 32306 no. surface atoms = 1581 nbur = 2106 mkacc time = 0.1600000 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 = 1.512000 m= 325 mr = 4038 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3284 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2813285E-10 -3.7159256E-10 midg,1,midg; midg,igrid,midg 1.3011214E-09 -4.0023423E-10 1,midg,midg; igrid,midg,midg -3.7976322E-10 1.1315668E-09 gauss-seidel spectral radius is 0.9833966 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 16:10:13 rms-change max change #iterations 8.9879066E-02 15.63598 at 10iterations 6.5119644E-03 1.021582 at 20iterations 5.5131072E-04 7.0793152E-02 at 30iterations 9.3561655E-05 1.2559891E-02 at 40iterations 2.6378450E-05 3.4556389E-03 at 50iterations finished qdiffx linear iterations at : 16:10:15 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 2.6378450E-05 3.4556389E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 16:10:16 3.237u 0.164s 0:03.68 92.1% 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 16:10:16 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.669167 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): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 1.669167 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 546.9006 centred at (gu) : 88.17403 90.59936 93.75107 assigned negative charge : -541.7030 centred at (gu) : 87.96777 90.82135 93.94423 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32306 grid for indexing accessible points = 1.400000 m= 27768 mr = 58519 m= 3176 mr = 19377 m= 93 mr = 1581 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 0.5800000 number of dielectric boundary points 35665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 27627 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) : 0.5563891 object centre at (A) : 32.09250 -2.330002 -4.886000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0950491E-03 1.1728127E-02 midg,1,midg; midg,igrid,midg 2.0623926E-02 1.4919093E-02 1,midg,midg; igrid,midg,midg -1.6661146E-05 1.5797865E-04 gauss-seidel spectral radius is 0.9983475 estimated iterations to convergence 195 setup time was (sec) 0.8600000 now iterating at: 16:10:17 rms-change max change #iterations 3.891995 157.1896 at 10iterations 1.688976 72.10247 at 20iterations 0.7346296 24.79399 at 30iterations 0.3178490 10.08018 at 40iterations 0.1381587 4.359028 at 50iterations 6.0023192E-02 1.921112 at 60iterations 2.6108906E-02 0.8256531 at 70iterations 1.1375184E-02 0.3816645 at 80iterations 4.9523185E-03 0.1730316 at 90iterations 2.1638495E-03 7.6879501E-02 at 100iterations 9.5024955E-04 3.6073685E-02 at 110iterations 4.2081586E-04 1.3019562E-02 at 120iterations finished qdiffx linear iterations at : 16:10:23 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 4.2081586E-04 1.3019562E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 16:10:23 7.154u 0.185s 0:07.62 96.1% 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 16:10:23 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3687 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN8 802 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.503751 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): 7.612999 56.57200 ymin,ymax (A): -34.32200 29.66200 zmin,zma (A): -35.55600 25.78400 x,y,z range (A): 48.95900 63.98400 61.34000 scale (grids/A): 2.503751 object centre (A): 32.09250 -2.330002 -4.886000 number of atom coordinates read : 3687 total number of charged atoms : 3583 net assigned charge : 5.200009 assigned positive charge : 546.9006 centred at (gu) : 87.26086 90.89873 95.62634 assigned negative charge : -541.7030 centred at (gu) : 86.95149 91.23198 95.91628 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 195334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32306 grid for indexing accessible points = 1.400000 m= 94353 mr = 142839 m= 28681 mr = 75291 m= 5021 mr = 21772 m= 384 mr = 3349 m= 11 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2977 time to turn everything in is 1.420000 number of dielectric boundary points 80395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 28640 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) : 1.669167 object centre at (A) : 32.09250 -2.330002 -4.886000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9825377E-02 0.4245183 midg,1,midg; midg,igrid,midg 0.2900828 0.3706414 1,midg,midg; igrid,midg,midg 1.9657934E-02 -2.2741938E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.720000 now iterating at: 16:10:25 rms-change max change #iterations 10.04149 330.0471 at 10iterations 5.830974 149.2453 at 20iterations 3.373511 76.29948 at 30iterations 1.940781 41.97808 at 40iterations 1.115523 23.03462 at 50iterations 0.6373976 11.99105 at 60iterations 0.3645211 7.288502 at 70iterations 0.2073449 4.011024 at 80iterations 0.1178204 2.087263 at 90iterations 6.6957377E-02 1.179899 at 100iterations 3.8005739E-02 0.7023745 at 110iterations 2.1511767E-02 0.4667873 at 120iterations 1.2211750E-02 0.2215729 at 130iterations 6.9045592E-03 0.1177120 at 140iterations 3.9118156E-03 7.4975967E-02 at 150iterations 2.2133302E-03 4.3453217E-02 at 160iterations 1.2485194E-03 2.3046494E-02 at 170iterations 7.0789002E-04 1.1974335E-02 at 180iterations finished qdiffx linear iterations at : 16:10:36 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 7.0789002E-04 1.1974335E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 16:10:37 12.707u 0.203s 0:13.18 97.8% 0+0k 0+0io 0pf+0w