Mon Oct 10 16:23:06 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 16:23:06 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 = 2344 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: 0.5856418 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 0.5856418 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 350.1211 centred at (gu) : 90.47466 90.40478 89.88443 assigned negative charge : -339.6217 centred at (gu) : 90.59479 90.48132 89.92973 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5284 nv = 96 ne = 84 npr = 46350 no. pairs analyzed = 46350 no. exposed pairs = 3234 no. arc points = 23337 no. surface atoms = 1087 nbur = 1257 mkacc time = 8.9999989E-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 = 1.456000 m= 248 mr = 2474 m= 0 mr = 15 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2440 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8200820E-09 1.8394910E-09 midg,1,midg; midg,igrid,midg 3.9611083E-09 1.3553287E-09 1,midg,midg; igrid,midg,midg 4.6695425E-09 3.6457692E-10 gauss-seidel spectral radius is 0.9849043 estimated iterations to convergence 67 setup time was (sec) 0.5000000 now iterating at: 16:23:06 rms-change max change #iterations 8.8675268E-02 16.40478 at 10iterations 7.2027720E-03 1.156914 at 20iterations 6.3385797E-04 0.1154442 at 30iterations 8.0543068E-05 1.9550323E-02 at 40iterations 1.6382613E-05 4.3640137E-03 at 50iterations finished qdiffx linear iterations at : 16:23:09 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.6382613E-05 4.3640137E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 16:23:09 3.117u 0.134s 0:03.54 91.5% 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 16:23:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.756925 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 1.756925 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 350.1211 centred at (gu) : 91.42374 91.21374 89.65305 assigned negative charge : -339.6217 centred at (gu) : 91.78420 91.44374 89.78922 start vw surface at 0.2000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56512 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23337 grid for indexing accessible points = 1.400000 m= 17145 mr = 34969 m= 2085 mr = 11511 m= 88 mr = 1085 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 28246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 17054 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) : 0.5856418 object centre at (A) : 228.3650 83.87900 188.0300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8240009E-03 1.9597795E-02 midg,1,midg; midg,igrid,midg 1.0681986E-02 8.8302363E-03 1,midg,midg; igrid,midg,midg 1.5557195E-02 6.7760064E-03 gauss-seidel spectral radius is 0.9983805 estimated iterations to convergence 197 setup time was (sec) 0.7400000 now iterating at: 16:23:10 rms-change max change #iterations 3.379156 182.7186 at 10iterations 1.471143 67.33627 at 20iterations 0.6411759 23.95930 at 30iterations 0.2801235 11.25888 at 40iterations 0.1221909 4.527504 at 50iterations 5.3340312E-02 2.044264 at 60iterations 2.3327192E-02 0.8904753 at 70iterations 1.0203483E-02 0.3991451 at 80iterations 4.4909706E-03 0.1778641 at 90iterations 1.9645728E-03 7.4972153E-02 at 100iterations 8.6979562E-04 3.5349846E-02 at 110iterations 3.8854484E-04 1.6929865E-02 at 120iterations finished qdiffx linear iterations at : 16:23:16 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 3.8854484E-04 1.6929865E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 16:23:17 6.822u 0.161s 0:07.25 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 Mon Oct 10 2011 at 16:23:17 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 = 2344 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.635388 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 2.635388 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 350.1211 centred at (gu) : 92.13551 91.82056 89.47945 assigned negative charge : -339.6217 centred at (gu) : 92.67625 92.16563 89.68382 start vw surface at 0.2000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 130327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23337 grid for indexing accessible points = 1.400000 m= 57919 mr = 86072 m= 17828 mr = 44321 m= 3421 mr = 13303 m= 375 mr = 2315 m= 12 mr = 219 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 63652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 17622 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) : 1.756925 object centre at (A) : 228.3650 83.87900 188.0300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5725437 0.2472433 midg,1,midg; midg,igrid,midg 9.3780264E-02 0.1041301 1,midg,midg; igrid,midg,midg 0.1497671 7.9498038E-02 gauss-seidel spectral radius is 0.9991898 estimated iterations to convergence 277 setup time was (sec) 1.300000 now iterating at: 16:23:18 rms-change max change #iterations 8.350117 272.3310 at 10iterations 4.755052 147.5293 at 20iterations 2.691427 66.55653 at 30iterations 1.512576 36.01802 at 40iterations 0.8519521 18.17806 at 50iterations 0.4762601 10.60143 at 60iterations 0.2664882 5.746956 at 70iterations 0.1489878 3.324716 at 80iterations 8.3286487E-02 1.717762 at 90iterations 4.6539612E-02 0.9713097 at 100iterations 2.5995774E-02 0.5691299 at 110iterations 1.4508589E-02 0.3283234 at 120iterations 8.1120348E-03 0.1843491 at 130iterations 4.5323921E-03 9.2855453E-02 at 140iterations 2.5399188E-03 5.7334900E-02 at 150iterations 1.4251441E-03 3.4879684E-02 at 160iterations 8.0198620E-04 1.6651154E-02 at 170iterations 4.5445270E-04 9.7455978E-03 at 180iterations finished qdiffx linear iterations at : 16:23:27 total time elapsed so far: 10.60000 # loops : 180 mean,max change (kT/e) : 4.5445270E-04 9.7455978E-03 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.81000 DelPhi exited at 16:23:28 10.816u 0.165s 0:11.26 97.4% 0+0k 0+0io 0pf+0w