Sat Oct 8 11:36:05 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 Sat Oct 8 2011 at 11:36:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5121713 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 0.5121713 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 588.8105 centred at (gu) : 88.18696 89.94676 91.16152 assigned negative charge : -596.8124 centred at (gu) : 88.20217 90.03355 91.23353 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 82381 no. pairs analyzed = 82381 no. exposed pairs = 4566 no. arc points = 30805 no. surface atoms = 1558 nbur = 2378 mkacc time = 0.2200000 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 = 1.652000 m= 216 mr = 3530 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.4200000 number of dielectric boundary points 3142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3103 ## 440 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1697180E-11 -3.9010373E-10 midg,1,midg; midg,igrid,midg 7.9285634E-11 -3.1745634E-10 1,midg,midg; igrid,midg,midg -1.3379370E-10 -9.7450749E-11 gauss-seidel spectral radius is 0.9804360 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 11:36:06 rms-change max change #iterations 6.1957218E-02 11.07489 at 10iterations 3.8980695E-03 0.7092438 at 20iterations 5.4786162E-04 8.4552765E-02 at 30iterations 1.5197773E-04 2.6107788E-02 at 40iterations 4.6532885E-05 8.2664490E-03 at 50iterations finished qdiffx linear iterations at : 11:36:10 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 4.6532885E-05 8.2664490E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 11:36:10 4.689u 0.381s 0:05.40 93.7% 0+0k 0+0io 6pf+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 8 2011 at 11:36:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 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: 1.536514 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 1.536514 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 588.8105 centred at (gu) : 84.55969 89.83922 93.48382 assigned negative charge : -596.8124 centred at (gu) : 84.60599 90.10024 93.70023 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30805 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21705 mr = 52636 m= 1927 mr = 14802 m= 34 mr = 859 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1577 time to turn everything in is 0.6000000 number of dielectric boundary points 29255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 28501 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) : 0.5121713 object centre at (A) : 32.77800 14.46600 10.70750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4814102E-03 -1.6273404E-02 midg,1,midg; midg,igrid,midg -1.6298991E-03 -8.4108757E-03 1,midg,midg; igrid,midg,midg 9.8111629E-03 -4.2937999E-03 gauss-seidel spectral radius is 0.9980230 estimated iterations to convergence 179 setup time was (sec) 0.8900000 now iterating at: 11:36:11 rms-change max change #iterations 3.421097 151.4751 at 10iterations 1.372726 53.69253 at 20iterations 0.5519497 19.47477 at 30iterations 0.2213986 9.138794 at 40iterations 8.9409009E-02 3.936382 at 50iterations 3.6202323E-02 1.261171 at 60iterations 1.4659715E-02 0.5345345 at 70iterations 5.9921374E-03 0.1983719 at 80iterations 2.5220653E-03 9.4764709E-02 at 90iterations 1.1181817E-03 4.2304993E-02 at 100iterations 5.5040658E-04 2.0286560E-02 at 110iterations 3.0296828E-04 1.1053562E-02 at 120iterations finished qdiffx linear iterations at : 11:36:21 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 3.0296828E-04 1.1053562E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 11:36:22 10.677u 0.450s 0:11.51 96.6% 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 8 2011 at 11:36:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3936 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.304771 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): -1.976000 67.53200 ymin,ymax (A): -9.862000 38.79400 zmin,zma (A): -19.63300 41.04800 x,y,z range (A): 69.50800 48.65600 60.68100 scale (grids/A): 2.304771 object centre (A): 32.77800 14.46600 10.70750 number of atom coordinates read : 3936 total number of charged atoms : 3783 net assigned charge : -7.999949 assigned positive charge : 588.8105 centred at (gu) : 81.83912 89.75840 95.22556 assigned negative charge : -596.8124 centred at (gu) : 81.90895 90.15018 95.55025 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30805 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 77956 mr = 128594 m= 19943 mr = 62121 m= 2804 mr = 14621 m= 123 mr = 1748 m= 0 mr = 24 time to grow re-entrant surface = 0.9100001 no. cavity mid-points inaccessible to solvent = 5307 time to turn everything in is 1.470000 number of dielectric boundary points 66033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 30196 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) : 1.536514 object centre at (A) : 32.77800 14.46600 10.70750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1158263 -0.2943443 midg,1,midg; midg,igrid,midg -4.4382840E-02 -0.1340089 1,midg,midg; igrid,midg,midg 0.4652779 -0.2721393 gauss-seidel spectral radius is 0.9991022 estimated iterations to convergence 264 setup time was (sec) 1.800000 now iterating at: 11:36:24 rms-change max change #iterations 9.143819 246.2518 at 10iterations 5.080988 148.2008 at 20iterations 2.807697 65.08952 at 30iterations 1.543056 31.46603 at 40iterations 0.8458472 16.64116 at 50iterations 0.4629653 9.960911 at 60iterations 0.2528691 5.772635 at 70iterations 0.1381090 2.842061 at 80iterations 7.5348794E-02 1.562717 at 90iterations 4.1069236E-02 0.9586692 at 100iterations 2.2352595E-02 0.4761047 at 110iterations 1.2189919E-02 0.2316227 at 120iterations 6.6691218E-03 0.1385536 at 130iterations 3.6668757E-03 7.3608398E-02 at 140iterations 2.0365454E-03 4.3744206E-02 at 150iterations 1.1537614E-03 2.4089813E-02 at 160iterations 6.7240628E-04 1.3496399E-02 at 170iterations 4.1130715E-04 8.9797974E-03 at 180iterations finished qdiffx linear iterations at : 11:36:39 total time elapsed so far: 17.32000 # loops : 180 mean,max change (kT/e) : 4.1130715E-04 8.9797974E-03 energy calculations done at 17.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.48000 DelPhi exited at 11:36:40 17.487u 0.461s 0:18.24 98.3% 0+0k 0+0io 0pf+0w