Mon Oct 10 19:39:08 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 Mon Oct 10 2011 at 19:39:08 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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: 0.6196045 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 0.6196045 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.028033 assigned positive charge : 364.5700 centred at (gu) : 88.65685 92.19277 91.69628 assigned negative charge : -359.5431 centred at (gu) : 88.64117 92.19806 91.67376 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6491 nv = 96 ne = 84 npr = 49111 no. pairs analyzed = 49111 no. exposed pairs = 3367 no. arc points = 23982 no. surface atoms = 1127 nbur = 1348 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3311 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2335 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8321058E-09 7.6783886E-09 midg,1,midg; midg,igrid,midg 2.6886791E-09 5.8163527E-09 1,midg,midg; igrid,midg,midg 3.9899373E-09 3.6748220E-09 gauss-seidel spectral radius is 0.9865103 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 19:39:09 rms-change max change #iterations 0.1228276 19.39763 at 10iterations 1.1189112E-02 2.140533 at 20iterations 1.0271592E-03 0.1500521 at 30iterations 9.5670024E-05 1.3761997E-02 at 40iterations 9.2768669E-06 1.4648438E-03 at 50iterations finished qdiffx linear iterations at : 19:39:12 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 9.2768669E-06 1.4648438E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 19:39:12 3.404u 0.166s 0:04.08 87.2% 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 Mon Oct 10 2011 at 19:39:12 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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: 1.858814 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 1.858814 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.028033 assigned positive charge : 364.5700 centred at (gu) : 85.96976 96.57780 95.08838 assigned negative charge : -359.5431 centred at (gu) : 85.92352 96.59420 95.02126 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 24025 mr = 46246 m= 3865 mr = 17192 m= 193 mr = 2265 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 32203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18372 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) : 0.6196045 object centre at (A) : 6.982999 -16.02800 41.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2810431E-03 1.9267661E-02 midg,1,midg; midg,igrid,midg 1.2365350E-02 -2.7546175E-03 1,midg,midg; igrid,midg,midg -4.6625170E-03 1.0945518E-02 gauss-seidel spectral radius is 0.9985613 estimated iterations to convergence 209 setup time was (sec) 0.5600000 now iterating at: 19:39:13 rms-change max change #iterations 3.873084 195.8734 at 10iterations 1.770982 61.58311 at 20iterations 0.8139076 26.39335 at 30iterations 0.3717824 12.51012 at 40iterations 0.1711479 5.866852 at 50iterations 7.8166962E-02 2.552743 at 60iterations 3.5778694E-02 1.401947 at 70iterations 1.6477546E-02 0.5408463 at 80iterations 7.5434530E-03 0.2377682 at 90iterations 3.4479913E-03 0.1469040 at 100iterations 1.5836934E-03 5.9147835E-02 at 110iterations 7.3148863E-04 2.6380539E-02 at 120iterations finished qdiffx linear iterations at : 19:39:20 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 7.3148863E-04 2.6380539E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 19:39:21 7.815u 0.210s 0:08.67 92.5% 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 19:39:21 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 !!! WARNING: HIR 323 has a net charge of 0.5140 !!! WARNING: HIR 449 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: 2.788220 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): -18.08500 32.05100 ymin,ymax (A): -42.90700 10.85100 zmin,zma (A): 13.25100 70.70700 x,y,z range (A): 50.13600 53.75800 57.45600 scale (grids/A): 2.788220 object centre (A): 6.982999 -16.02800 41.97900 number of atom coordinates read : 2475 total number of charged atoms : 2337 net assigned charge : 5.028033 assigned positive charge : 364.5700 centred at (gu) : 83.95465 99.86642 97.63251 assigned negative charge : -359.5431 centred at (gu) : 83.88532 99.89137 97.53197 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 77502 mr = 113086 m= 28194 mr = 61818 m= 6771 mr = 22182 m= 860 mr = 4824 m= 38 mr = 494 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 72758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 18694 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) : 1.858814 object centre at (A) : 6.982999 -16.02800 41.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9288518E-02 0.2288711 midg,1,midg; midg,igrid,midg 0.1648059 -5.1518209E-02 1,midg,midg; igrid,midg,midg -0.1280202 0.1491559 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.120000 now iterating at: 19:39:23 rms-change max change #iterations 9.253657 319.3945 at 10iterations 5.351164 127.5232 at 20iterations 3.077744 59.88306 at 30iterations 1.766454 36.17097 at 40iterations 1.011815 21.34891 at 50iterations 0.5807769 10.84393 at 60iterations 0.3317022 6.524326 at 70iterations 0.1897878 4.119680 at 80iterations 0.1079560 1.966208 at 90iterations 6.1465200E-02 1.251228 at 100iterations 3.5103656E-02 0.6676865 at 110iterations 2.0012988E-02 0.4274769 at 120iterations 1.1374101E-02 0.2123933 at 130iterations 6.4814286E-03 0.1192017 at 140iterations 3.6865859E-03 6.5345764E-02 at 150iterations 2.0998858E-03 3.8815022E-02 at 160iterations 1.1947950E-03 2.1560669E-02 at 170iterations 6.8101985E-04 1.3463974E-02 at 180iterations finished qdiffx linear iterations at : 19:39:34 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 6.8101985E-04 1.3463974E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 19:39:34 12.668u 0.212s 0:13.32 96.6% 0+0k 0+0io 0pf+0w