Wed Dec 21 14:21:14 PST 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 Wed Dec 21 2011 at 14:21:14 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 = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 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: 0.6459339 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 0.6459339 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 283.8521 centred at (gu) : 90.48875 92.32444 90.05859 assigned negative charge : -283.7923 centred at (gu) : 90.54588 92.45244 90.03117 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 40154 no. pairs analyzed = 40154 no. exposed pairs = 2417 no. arc points = 16831 no. surface atoms = 827 nbur = 1119 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3143 m= 0 mr = 42 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2600000 number of dielectric boundary points 2690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2308495E-09 3.2354326E-09 midg,1,midg; midg,igrid,midg 7.9370972E-09 -2.0724087E-08 1,midg,midg; igrid,midg,midg 5.5093929E-09 -5.8277680E-09 gauss-seidel spectral radius is 0.9875222 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 14:21:15 rms-change max change #iterations 0.1260537 23.84535 at 10iterations 1.2689910E-02 2.044438 at 20iterations 1.2826736E-03 0.1944032 at 30iterations 1.2825274E-04 2.0397186E-02 at 40iterations 1.3139862E-05 1.9264221E-03 at 50iterations finished qdiffx linear iterations at : 14:21:21 total time elapsed so far: 7.210000 # loops : 50 mean,max change (kT/e) : 1.3139862E-05 1.9264221E-03 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 14:21:26 7.403u 0.491s 0:12.96 60.8% 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 Wed Dec 21 2011 at 14:21:28 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 = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.937802 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 1.937802 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 283.8521 centred at (gu) : 91.46632 96.97317 90.17581 assigned negative charge : -283.7923 centred at (gu) : 91.63788 97.35737 90.09356 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16831 grid for indexing accessible points = 1.400000 m= 21945 mr = 41494 m= 3280 mr = 16785 m= 153 mr = 2142 m= 0 mr = 49 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1446 time to turn everything in is 0.4900000 number of dielectric boundary points 24624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14332 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) : 0.6459339 object centre at (A) : 15.06300 22.75950 3.358001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5177184E-02 9.3212454E-03 midg,1,midg; midg,igrid,midg 2.1754226E-02 -1.8343190E-02 1,midg,midg; igrid,midg,midg 2.1977623E-03 -4.6079159E-03 gauss-seidel spectral radius is 0.9985993 estimated iterations to convergence 212 setup time was (sec) 0.7800000 now iterating at: 14:21:30 rms-change max change #iterations 3.637740 179.5392 at 10iterations 1.680294 62.32968 at 20iterations 0.7825294 29.93178 at 30iterations 0.3637982 13.91767 at 40iterations 0.1681640 5.945309 at 50iterations 7.7606894E-02 2.665237 at 60iterations 3.5863295E-02 1.432249 at 70iterations 1.6728241E-02 0.5825577 at 80iterations 7.7379472E-03 0.2633362 at 90iterations 3.5986460E-03 0.1273017 at 100iterations 1.6636342E-03 5.9524536E-02 at 110iterations 7.7274110E-04 2.5434494E-02 at 120iterations finished qdiffx linear iterations at : 14:21:47 total time elapsed so far: 17.97000 # loops : 120 mean,max change (kT/e) : 7.7274110E-04 2.5434494E-02 energy calculations done at 17.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.15000 DelPhi exited at 14:21:57 18.151u 0.547s 0:29.76 62.8% 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 Wed Dec 21 2011 at 14:21:59 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 = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 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: 2.906703 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 2.906703 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 283.8521 centred at (gu) : 92.19940 100.4598 90.26368 assigned negative charge : -283.7923 centred at (gu) : 92.45687 101.0361 90.14037 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 137960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16831 grid for indexing accessible points = 1.400000 m= 70942 mr = 100283 m= 25732 mr = 59102 m= 5934 mr = 21374 m= 730 mr = 4576 m= 35 mr = 474 m= 0 mr = 10 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 5133 time to turn everything in is 1.330000 number of dielectric boundary points 55514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 14506 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) : 1.937802 object centre at (A) : 15.06300 22.75950 3.358001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.098883 6.2154173E-03 midg,1,midg; midg,igrid,midg 0.1760116 -0.2246634 1,midg,midg; igrid,midg,midg 9.0721399E-03 -2.5894942E-02 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.740000 now iterating at: 14:22:02 rms-change max change #iterations 8.514038 357.4409 at 10iterations 4.896598 129.4511 at 20iterations 2.793316 61.96167 at 30iterations 1.593308 37.52534 at 40iterations 0.9088901 20.60153 at 50iterations 0.5158705 11.09127 at 60iterations 0.2949678 8.093765 at 70iterations 0.1674705 3.740924 at 80iterations 9.5412560E-02 2.021214 at 90iterations 5.4199126E-02 1.220756 at 100iterations 3.0850852E-02 0.6657190 at 110iterations 1.7519044E-02 0.3733063 at 120iterations 9.9492222E-03 0.2106476 at 130iterations 5.6508114E-03 0.1129112 at 140iterations 3.2127465E-03 6.4983368E-02 at 150iterations 1.8239456E-03 3.7017822E-02 at 160iterations 1.0372342E-03 2.1306992E-02 at 170iterations 5.9081591E-04 1.1404991E-02 at 180iterations finished qdiffx linear iterations at : 14:22:31 total time elapsed so far: 31.19000 # loops : 180 mean,max change (kT/e) : 5.9081591E-04 1.1404991E-02 energy calculations done at 31.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.36000 DelPhi exited at 14:22:38 31.367u 0.546s 0:38.69 82.4% 0+0k 0+0io 0pf+0w