Mon Oct 10 16:03:43 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 Mon Oct 10 2011 at 16:03:43 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 = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5467502 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 0.5467502 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 653.5630 centred at (gu) : 90.20099 89.69435 91.57333 assigned negative charge : -648.0663 centred at (gu) : 90.24587 89.65990 91.60143 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 86500 no. pairs analyzed = 86500 no. exposed pairs = 5378 no. arc points = 36603 no. surface atoms = 1804 nbur = 2518 mkacc time = 0.1500000 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 = 1.568000 m= 363 mr = 4679 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2800000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3757 ## 493 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 11221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3511358E-10 1.0774800E-10 midg,1,midg; midg,igrid,midg 1.4898050E-11 6.4963845E-10 1,midg,midg; igrid,midg,midg 7.6412482E-10 -9.5191854E-11 gauss-seidel spectral radius is 0.9828537 estimated iterations to convergence 63 setup time was (sec) 0.4700000 now iterating at: 16:03:43 rms-change max change #iterations 9.1070905E-02 13.33239 at 10iterations 6.5316265E-03 0.8891497 at 20iterations 9.5121370E-04 0.1745758 at 30iterations 3.4513630E-04 5.2825928E-02 at 40iterations 1.4673898E-04 2.0448685E-02 at 50iterations finished qdiffx linear iterations at : 16:03:46 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.4673898E-04 2.0448685E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:03:47 3.455u 0.174s 0:04.06 89.1% 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 Mon Oct 10 2011 at 16:03:47 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 = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.640251 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 1.640251 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 653.5630 centred at (gu) : 90.60164 89.08160 94.71852 assigned negative charge : -648.0663 centred at (gu) : 90.73733 88.97903 94.80407 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 94751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30655 mr = 67014 m= 3322 mr = 21375 m= 106 mr = 1651 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 418 time to turn everything in is 0.4500000 number of dielectric boundary points 38788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 32331 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) : 0.5467502 object centre at (A) : -33.18350 2.248000 -3.422001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6042303E-03 1.4271685E-02 midg,1,midg; midg,igrid,midg 2.0412527E-02 1.8425440E-02 1,midg,midg; igrid,midg,midg 1.7667158E-03 6.1839650E-04 gauss-seidel spectral radius is 0.9983412 estimated iterations to convergence 195 setup time was (sec) 0.6700000 now iterating at: 16:03:48 rms-change max change #iterations 4.152285 181.6672 at 10iterations 1.797085 52.43269 at 20iterations 0.7814451 26.50753 at 30iterations 0.3388472 9.945301 at 40iterations 0.1472507 4.649559 at 50iterations 6.4127259E-02 2.083920 at 60iterations 2.7915558E-02 0.8353500 at 70iterations 1.2208263E-02 0.4068794 at 80iterations 5.3721513E-03 0.1487622 at 90iterations 2.4255908E-03 7.4798584E-02 at 100iterations 1.1498727E-03 4.0496826E-02 at 110iterations 6.0467649E-04 1.9023895E-02 at 120iterations finished qdiffx linear iterations at : 16:03:55 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 6.0467649E-04 1.9023895E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 16:03:55 7.874u 0.198s 0:08.35 96.5% 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 Mon Oct 10 2011 at 16:03:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4322 !!! WARNING: ASP 607 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.460376 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): -58.93400 -7.433000 ymin,ymax (A): -29.76800 34.26400 zmin,zma (A): -35.97800 29.13400 x,y,z range (A): 51.50100 64.03200 65.11200 scale (grids/A): 2.460376 object centre (A): -33.18350 2.248000 -3.422001 number of atom coordinates read : 4322 total number of charged atoms : 4223 net assigned charge : 5.500020 assigned positive charge : 653.5630 centred at (gu) : 90.90212 88.62209 97.07748 assigned negative charge : -648.0663 centred at (gu) : 91.10574 88.46835 97.20597 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 220454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36603 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105620 mr = 163684 m= 30873 mr = 84216 m= 5166 mr = 23325 m= 439 mr = 3408 m= 4 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 1364 time to turn everything in is 1.130000 number of dielectric boundary points 87759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 33753 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) : 1.640251 object centre at (A) : -33.18350 2.248000 -3.422001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7014854E-02 0.5275174 midg,1,midg; midg,igrid,midg 0.4219365 0.2533659 1,midg,midg; igrid,midg,midg 4.2548746E-02 2.5884574E-02 gauss-seidel spectral radius is 0.9992219 estimated iterations to convergence 283 setup time was (sec) 1.380000 now iterating at: 16:03:57 rms-change max change #iterations 10.80861 328.0244 at 10iterations 6.314061 139.5119 at 20iterations 3.675132 77.54439 at 30iterations 2.128319 43.85275 at 40iterations 1.227255 25.31623 at 50iterations 0.7053020 13.31417 at 60iterations 0.4046000 7.237240 at 70iterations 0.2314612 4.012396 at 80iterations 0.1323005 2.297998 at 90iterations 7.5589046E-02 1.399782 at 100iterations 4.3134172E-02 0.7102890 at 110iterations 2.4598340E-02 0.4291992 at 120iterations 1.4011952E-02 0.2520256 at 130iterations 7.9976963E-03 0.1504936 at 140iterations 4.5824903E-03 7.7899933E-02 at 150iterations 2.6361346E-03 4.8334122E-02 at 160iterations 1.5330084E-03 2.6300430E-02 at 170iterations 9.1365539E-04 1.7908096E-02 at 180iterations finished qdiffx linear iterations at : 16:04:09 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 9.1365539E-04 1.7908096E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 16:04:09 13.400u 0.280s 0:13.96 97.9% 0+0k 0+0io 0pf+0w