Sat Oct 15 14:26:51 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 Sat Oct 15 2011 at 14:26:51 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 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: 0.6381072 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): -8.510000 47.28000 ymin,ymax (A): -7.199000 41.51000 zmin,zma (A): 0.5340000 55.13100 x,y,z range (A): 55.79000 48.70900 54.59700 scale (grids/A): 0.6381072 object centre (A): 19.38500 17.15550 27.83250 number of atom coordinates read : 2986 total number of charged atoms : 2844 net assigned charge : -4.485968 assigned positive charge : 451.9088 centred at (gu) : 89.60339 89.39861 88.60575 assigned negative charge : -456.3961 centred at (gu) : 89.57147 89.28530 88.50090 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8115 nv = 96 ne = 84 npr = 60860 no. pairs analyzed = 60860 no. exposed pairs = 3854 no. arc points = 26959 no. surface atoms = 1309 nbur = 1677 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4322 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2200000 number of dielectric boundary points 4175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2689 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6528587E-08 5.5739986E-09 midg,1,midg; midg,igrid,midg -2.3603178E-08 7.6064923E-09 1,midg,midg; igrid,midg,midg -1.0857907E-08 -1.5773985E-09 gauss-seidel spectral radius is 0.9873137 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:26:52 rms-change max change #iterations 0.1533224 22.11232 at 10iterations 1.5014183E-02 1.831192 at 20iterations 1.4900434E-03 0.2000446 at 30iterations 1.5280557E-04 1.9188881E-02 at 40iterations 1.8288367E-05 3.2176971E-03 at 50iterations finished qdiffx linear iterations at : 14:26:55 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.8288367E-05 3.2176971E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 14:26:55 3.749u 0.232s 0:04.24 93.6% 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 Sat Oct 15 2011 at 14:26:55 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 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: 1.914322 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): -8.510000 47.28000 ymin,ymax (A): -7.199000 41.51000 zmin,zma (A): 0.5340000 55.13100 x,y,z range (A): 55.79000 48.70900 54.59700 scale (grids/A): 1.914322 object centre (A): 19.38500 17.15550 27.83250 number of atom coordinates read : 2986 total number of charged atoms : 2844 net assigned charge : -4.485968 assigned positive charge : 451.9088 centred at (gu) : 88.80970 88.19505 85.81638 assigned negative charge : -456.3961 centred at (gu) : 88.71387 87.85565 85.50212 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87284 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26959 grid for indexing accessible points = 1.400000 m= 30012 mr = 59226 m= 4625 mr = 21576 m= 256 mr = 2803 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2065 time to turn everything in is 0.4500000 number of dielectric boundary points 38487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 22399 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) : 0.6381072 object centre at (A) : 19.38500 17.15550 27.83250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9336459E-03 1.5169605E-02 midg,1,midg; midg,igrid,midg -3.6979042E-02 4.7437334E-03 1,midg,midg; igrid,midg,midg -6.3556038E-02 1.8993793E-02 gauss-seidel spectral radius is 0.9986870 estimated iterations to convergence 219 setup time was (sec) 0.7200000 now iterating at: 14:26:56 rms-change max change #iterations 4.686502 186.3159 at 10iterations 2.228382 78.07423 at 20iterations 1.057534 33.50586 at 30iterations 0.5013797 16.53240 at 40iterations 0.2376315 6.683121 at 50iterations 0.1129430 3.165641 at 60iterations 5.3540155E-02 1.815948 at 70iterations 2.5458608E-02 0.6996005 at 80iterations 1.2142762E-02 0.3500900 at 90iterations 5.7509081E-03 0.1713204 at 100iterations 2.7311575E-03 8.1648827E-02 at 110iterations 1.2972845E-03 4.1099548E-02 at 120iterations finished qdiffx linear iterations at : 14:27:05 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 1.2972845E-03 4.1099548E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 14:27:05 8.983u 0.257s 0:09.77 94.4% 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 Sat Oct 15 2011 at 14:27:05 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 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: 2.871482 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): -8.510000 47.28000 ymin,ymax (A): -7.199000 41.51000 zmin,zma (A): 0.5340000 55.13100 x,y,z range (A): 55.79000 48.70900 54.59700 scale (grids/A): 2.871482 object centre (A): 19.38500 17.15550 27.83250 number of atom coordinates read : 2986 total number of charged atoms : 2844 net assigned charge : -4.485968 assigned positive charge : 451.9088 centred at (gu) : 88.21427 87.29244 83.72429 assigned negative charge : -456.3961 centred at (gu) : 88.07050 86.78333 83.25302 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 201832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26959 grid for indexing accessible points = 1.400000 m= 98057 mr = 143885 m= 34440 mr = 79003 m= 7997 mr = 27229 m= 1133 mr = 5906 m= 77 mr = 751 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 7171 time to turn everything in is 1.210000 number of dielectric boundary points 86725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 22748 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) : 1.914322 object centre at (A) : 19.38500 17.15550 27.83250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2876756 -5.7945713E-02 midg,1,midg; midg,igrid,midg -0.3317875 4.9086828E-02 1,midg,midg; igrid,midg,midg -0.7793174 0.3918830 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.520000 now iterating at: 14:27:07 rms-change max change #iterations 11.20947 419.5775 at 10iterations 6.730763 156.1341 at 20iterations 3.991644 91.58534 at 30iterations 2.360628 46.82260 at 40iterations 1.391157 29.23084 at 50iterations 0.8165393 15.55083 at 60iterations 0.4790931 8.933105 at 70iterations 0.2812855 5.345428 at 80iterations 0.1638581 2.845018 at 90iterations 9.5765203E-02 1.643500 at 100iterations 5.6039821E-02 0.9276614 at 110iterations 3.2619648E-02 0.5550289 at 120iterations 1.9086819E-02 0.3473511 at 130iterations 1.1103680E-02 0.2026243 at 140iterations 6.4834035E-03 0.1203120 at 150iterations 3.7770190E-03 6.5674305E-02 at 160iterations 2.1974866E-03 3.6244392E-02 at 170iterations 1.2825445E-03 2.1713734E-02 at 180iterations finished qdiffx linear iterations at : 14:27:21 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 1.2825445E-03 2.1713734E-02 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.80000 DelPhi exited at 14:27:22 15.800u 0.306s 0:16.42 98.0% 0+0k 0+0io 0pf+0w