Sun Oct 9 06:36:09 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 06:36:09 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 0.6719897 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 0.6719897 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500012 assigned positive charge : 293.4370 centred at (gu) : 89.83781 89.34233 88.30876 assigned negative charge : -291.9371 centred at (gu) : 89.63255 89.21595 88.20233 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5915 nv = 96 ne = 84 npr = 40333 no. pairs analyzed = 40333 no. exposed pairs = 2431 no. arc points = 17258 no. surface atoms = 820 nbur = 1134 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3217 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2600000 number of dielectric boundary points 2995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1612 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2458661E-08 1.9156651E-08 midg,1,midg; midg,igrid,midg -2.2663647E-08 2.7049031E-08 1,midg,midg; igrid,midg,midg -3.7326057E-08 4.4720405E-08 gauss-seidel spectral radius is 0.9884613 estimated iterations to convergence 76 setup time was (sec) 0.5000000 now iterating at: 06:36:10 rms-change max change #iterations 0.1564446 25.20018 at 10iterations 1.7165180E-02 2.623177 at 20iterations 1.8909100E-03 0.3177452 at 30iterations 2.0388486E-04 3.1065464E-02 at 40iterations 2.2523463E-05 3.5448074E-03 at 50iterations finished qdiffx linear iterations at : 06:36:12 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.2523463E-05 3.5448074E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:36:13 3.345u 0.220s 0:03.86 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 06:36:13 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 2.015969 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 2.015969 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500012 assigned positive charge : 293.4370 centred at (gu) : 89.51313 88.02700 84.92648 assigned negative charge : -291.9371 centred at (gu) : 88.89764 87.64782 84.60721 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 23800 mr = 42850 m= 4268 mr = 17925 m= 330 mr = 2860 m= 3 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 933 time to turn everything in is 0.4800000 number of dielectric boundary points 27531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14347 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) : 0.6719897 object centre at (A) : 23.24350 14.14850 1.984500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1636800E-02 3.4475423E-02 midg,1,midg; midg,igrid,midg -1.8110676E-02 8.4544886E-03 1,midg,midg; igrid,midg,midg -2.7840158E-02 3.6430132E-02 gauss-seidel spectral radius is 0.9987099 estimated iterations to convergence 221 setup time was (sec) 0.7700000 now iterating at: 06:36:14 rms-change max change #iterations 4.070781 187.7258 at 10iterations 1.941633 67.98671 at 20iterations 0.9265035 33.61659 at 30iterations 0.4428227 14.78525 at 40iterations 0.2117694 7.025669 at 50iterations 0.1014225 3.295322 at 60iterations 4.8411060E-02 1.628762 at 70iterations 2.3158137E-02 0.7557039 at 80iterations 1.1004064E-02 0.3997593 at 90iterations 5.2912165E-03 0.1638765 at 100iterations 2.5311303E-03 8.3745956E-02 at 110iterations 1.2069371E-03 4.1679859E-02 at 120iterations finished qdiffx linear iterations at : 06:36:20 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.2069371E-03 4.1679859E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 06:36:21 7.649u 0.253s 0:08.25 95.6% 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 Sun Oct 9 2011 at 06:36:21 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 3.023954 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 3.023954 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500012 assigned positive charge : 293.4370 centred at (gu) : 89.26970 87.04043 82.38990 assigned negative charge : -291.9371 centred at (gu) : 88.34652 86.47173 81.91078 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 144870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 75096 mr = 103438 m= 29545 mr = 61919 m= 8103 mr = 24290 m= 1383 mr = 6407 m= 100 mr = 944 m= 3 mr = 48 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 3057 time to turn everything in is 1.190000 number of dielectric boundary points 62055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14520 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) : 2.015969 object centre at (A) : 23.24350 14.14850 1.984500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6303563 0.7489709 midg,1,midg; midg,igrid,midg -0.1086194 9.9890098E-02 1,midg,midg; igrid,midg,midg -0.2424646 0.3236919 gauss-seidel spectral radius is 0.9992625 estimated iterations to convergence 291 setup time was (sec) 1.510000 now iterating at: 06:36:23 rms-change max change #iterations 9.281885 411.1715 at 10iterations 5.359946 120.9906 at 20iterations 3.095480 66.29331 at 30iterations 1.786637 33.66256 at 40iterations 1.027971 22.34278 at 50iterations 0.5907244 13.43870 at 60iterations 0.3403571 6.183331 at 70iterations 0.1955695 3.661261 at 80iterations 0.1121330 2.661774 at 90iterations 6.4460792E-02 1.186089 at 100iterations 3.7066903E-02 0.7390823 at 110iterations 2.1330550E-02 0.3976028 at 120iterations 1.2185755E-02 0.2569151 at 130iterations 7.0156399E-03 0.1315763 at 140iterations 4.0345099E-03 7.7304840E-02 at 150iterations 2.3189520E-03 4.4209480E-02 at 160iterations 1.3280842E-03 2.4349213E-02 at 170iterations 7.6391391E-04 1.3900757E-02 at 180iterations finished qdiffx linear iterations at : 06:36:33 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 7.6391391E-04 1.3900757E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 06:36:34 12.326u 0.277s 0:12.88 97.7% 0+0k 0+0io 0pf+0w