Sun Oct 9 09:56:09 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 09:56:09 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 208 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5824321 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 0.5824321 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.985980 assigned positive charge : 387.3514 centred at (gu) : 88.14680 89.66182 89.86454 assigned negative charge : -393.3389 centred at (gu) : 88.19721 89.68130 90.08438 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6192 nv = 96 ne = 84 npr = 53991 no. pairs analyzed = 53991 no. exposed pairs = 3691 no. arc points = 26536 no. surface atoms = 1242 nbur = 1456 mkacc time = 9.9999994E-02 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= 349 mr = 3092 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2481 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1656573E-09 -5.9961875E-09 midg,1,midg; midg,igrid,midg -1.1143875E-09 -1.7157350E-09 1,midg,midg; igrid,midg,midg -5.5790755E-10 -1.6434861E-09 gauss-seidel spectral radius is 0.9847742 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 09:56:10 rms-change max change #iterations 9.4215445E-02 16.44950 at 10iterations 7.3725823E-03 1.188697 at 20iterations 5.8584777E-04 8.8500977E-02 at 30iterations 4.7271642E-05 7.4691772E-03 at 40iterations 3.8572275E-06 5.4931641E-04 at 50iterations finished qdiffx linear iterations at : 09:56:13 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.8572275E-06 5.4931641E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 09:56:13 3.554u 0.200s 0:04.03 93.0% 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 09:56:13 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 208 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.747296 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 1.747296 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.985980 assigned positive charge : 387.3514 centred at (gu) : 84.43984 88.98463 89.59267 assigned negative charge : -393.3389 centred at (gu) : 84.59174 89.04393 90.25320 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26536 grid for indexing accessible points = 1.400000 m= 22390 mr = 44200 m= 3242 mr = 15420 m= 138 mr = 1800 m= 0 mr = 18 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 629 time to turn everything in is 0.3500000 number of dielectric boundary points 31797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19794 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) : 0.5824321 object centre at (A) : 62.55750 38.49850 69.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4761794E-03 -3.6220271E-02 midg,1,midg; midg,igrid,midg -9.8178992E-03 -8.0190329E-03 1,midg,midg; igrid,midg,midg 1.0171671E-02 -1.1338844E-02 gauss-seidel spectral radius is 0.9984118 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 09:56:14 rms-change max change #iterations 3.603498 160.7813 at 10iterations 1.577144 62.34941 at 20iterations 0.6943833 25.44308 at 30iterations 0.3062006 10.26511 at 40iterations 0.1350321 4.656936 at 50iterations 5.9430566E-02 1.971008 at 60iterations 2.6182856E-02 0.9807243 at 70iterations 1.1538701E-02 0.4025245 at 80iterations 5.0984165E-03 0.1792164 at 90iterations 2.2534025E-03 7.9765320E-02 at 100iterations 9.8845118E-04 3.5903931E-02 at 110iterations 4.3858090E-04 1.5136719E-02 at 120iterations finished qdiffx linear iterations at : 09:56:22 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 4.3858090E-04 1.5136719E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 09:56:22 8.133u 0.230s 0:08.69 96.2% 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 09:56:22 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 208 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.620944 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): 35.11300 90.00200 ymin,ymax (A): 7.937000 69.06001 zmin,zma (A): 44.87500 95.02900 x,y,z range (A): 54.88900 61.12300 50.15400 scale (grids/A): 2.620944 object centre (A): 62.55750 38.49850 69.95200 number of atom coordinates read : 2698 total number of charged atoms : 2536 net assigned charge : -5.985980 assigned positive charge : 387.3514 centred at (gu) : 81.65959 88.47678 89.38896 assigned negative charge : -393.3389 centred at (gu) : 81.88749 88.56582 90.37990 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26536 grid for indexing accessible points = 1.400000 m= 73396 mr = 108325 m= 25113 mr = 57400 m= 5555 mr = 19219 m= 628 mr = 3896 m= 18 mr = 321 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2105 time to turn everything in is 0.8500000 number of dielectric boundary points 71601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20279 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) : 1.747296 object centre at (A) : 62.55750 38.49850 69.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4623259E-02 -0.4725247 midg,1,midg; midg,igrid,midg -0.1121106 -8.8041052E-02 1,midg,midg; igrid,midg,midg 0.1417734 -0.2174972 gauss-seidel spectral radius is 0.9992023 estimated iterations to convergence 280 setup time was (sec) 1.100000 now iterating at: 09:56:23 rms-change max change #iterations 8.978320 306.9659 at 10iterations 5.192962 132.6272 at 20iterations 2.974330 67.92671 at 30iterations 1.699487 44.57975 at 40iterations 0.9662719 21.58326 at 50iterations 0.5470149 10.96982 at 60iterations 0.3088641 6.899634 at 70iterations 0.1744703 3.503546 at 80iterations 9.8316744E-02 2.148995 at 90iterations 5.5578433E-02 1.143337 at 100iterations 3.1211210E-02 0.6267576 at 110iterations 1.7619772E-02 0.3361987 at 120iterations 9.8873461E-03 0.1891575 at 130iterations 5.5644577E-03 0.1068306 at 140iterations 3.1389818E-03 6.1556816E-02 at 150iterations 1.7662406E-03 3.5499573E-02 at 160iterations 9.9704473E-04 2.0503998E-02 at 170iterations 5.6200800E-04 1.1738777E-02 at 180iterations finished qdiffx linear iterations at : 09:56:35 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 5.6200800E-04 1.1738777E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 09:56:36 13.041u 0.234s 0:13.55 97.9% 0+0k 0+0io 0pf+0w