Sun Oct 9 19:13:06 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+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 19:13:06 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5591857 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 0.5591857 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.754032 assigned positive charge : 741.5269 centred at (gu) : 88.26415 89.53381 89.43425 assigned negative charge : -738.7777 centred at (gu) : 88.12316 89.56448 89.38541 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 10022 nv = 96 ne = 84 npr = 98802 no. pairs analyzed = 98802 no. exposed pairs = 5687 no. arc points = 38415 no. surface atoms = 1952 nbur = 2914 mkacc time = 0.1700000 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 = 1.540000 m= 477 mr = 5788 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3963 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 13055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2130329E-10 1.0467356E-09 midg,1,midg; midg,igrid,midg 9.8648367E-10 -1.8745233E-10 1,midg,midg; igrid,midg,midg -3.4283394E-09 1.8404896E-09 gauss-seidel spectral radius is 0.9836441 estimated iterations to convergence 64 setup time was (sec) 0.5000000 now iterating at: 19:13:06 rms-change max change #iterations 0.1134994 14.06265 at 10iterations 1.5623362E-02 1.965515 at 20iterations 6.4059398E-03 0.8908157 at 30iterations 3.0712048E-03 0.4298019 at 40iterations 1.4894606E-03 0.2064285 at 50iterations finished qdiffx linear iterations at : 19:13:09 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.4894606E-03 0.2064285 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 19:13:10 3.509u 0.209s 0:03.98 92.9% 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 19:13:10 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.677557 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 1.677557 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.754032 assigned positive charge : 741.5269 centred at (gu) : 84.79134 88.60010 88.30155 assigned negative charge : -738.7777 centred at (gu) : 84.36928 88.69334 88.15599 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 112117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38415 grid for indexing accessible points = 1.400000 m= 39297 mr = 81496 m= 4947 mr = 28586 m= 181 mr = 2703 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 43733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 36222 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) : 0.5591857 object centre at (A) : 34.01100 21.73950 29.68200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8937755E-02 -2.2318889E-03 midg,1,midg; midg,igrid,midg 1.3782426E-02 1.1204928E-02 1,midg,midg; igrid,midg,midg -1.6398549E-02 3.7924860E-02 gauss-seidel spectral radius is 0.9984615 estimated iterations to convergence 202 setup time was (sec) 0.7400000 now iterating at: 19:13:11 rms-change max change #iterations 4.758919 179.0917 at 10iterations 2.130079 66.35736 at 20iterations 0.9522070 28.05353 at 30iterations 0.4287608 11.60013 at 40iterations 0.1934749 5.433588 at 50iterations 8.8541560E-02 2.699347 at 60iterations 4.2335976E-02 1.277031 at 70iterations 2.2013554E-02 0.7165031 at 80iterations 1.2874155E-02 0.4020882 at 90iterations 8.7003652E-03 0.2614059 at 100iterations 6.3457587E-03 0.1852188 at 110iterations 4.7919312E-03 0.1362686 at 120iterations finished qdiffx linear iterations at : 19:13:18 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 4.7919312E-03 0.1362686 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 19:13:18 8.099u 0.215s 0:08.58 96.7% 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 19:13:18 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4866 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.516336 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): 3.436000 64.58600 ymin,ymax (A): -8.897000 52.37600 zmin,zma (A): -2.150000 61.51400 x,y,z range (A): 61.15000 61.27300 63.66400 scale (grids/A): 2.516336 object centre (A): 34.01100 21.73950 29.68200 number of atom coordinates read : 4866 total number of charged atoms : 4693 net assigned charge : 2.754032 assigned positive charge : 741.5269 centred at (gu) : 82.18667 87.89981 87.45216 assigned negative charge : -738.7777 centred at (gu) : 81.55397 88.03993 87.23411 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 260697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38415 grid for indexing accessible points = 1.400000 m= 132364 mr = 198314 m= 42330 mr = 108348 m= 8117 mr = 32996 m= 741 mr = 5586 m= 14 mr = 432 m= 0 mr = 2 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 98585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 37496 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) : 1.677557 object centre at (A) : 34.01100 21.73950 29.68200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3502636 6.7701526E-02 midg,1,midg; midg,igrid,midg -1.0913029E-02 -1.3925465E-02 1,midg,midg; igrid,midg,midg -0.3419855 0.6091521 gauss-seidel spectral radius is 0.9992583 estimated iterations to convergence 290 setup time was (sec) 1.620000 now iterating at: 19:13:20 rms-change max change #iterations 12.10323 301.1172 at 10iterations 7.159285 140.0765 at 20iterations 4.200994 84.35072 at 30iterations 2.456375 43.14229 at 40iterations 1.433564 27.58979 at 50iterations 0.8320305 13.47595 at 60iterations 0.4825140 8.157408 at 70iterations 0.2798252 4.766251 at 80iterations 0.1621480 2.611713 at 90iterations 9.4186269E-02 1.602657 at 100iterations 5.5292740E-02 0.9581316 at 110iterations 3.3005480E-02 0.5338345 at 120iterations 2.0299623E-02 0.3848648 at 130iterations 1.3187375E-02 0.2541199 at 140iterations 9.1893580E-03 0.1682816 at 150iterations 6.8876147E-03 0.1201591 at 160iterations 5.4616476E-03 9.4696045E-02 at 170iterations 4.4756238E-03 7.5508118E-02 at 180iterations finished qdiffx linear iterations at : 19:13:32 total time elapsed so far: 13.49000 # loops : 180 mean,max change (kT/e) : 4.4756238E-03 7.5508118E-02 energy calculations done at 13.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 19:13:32 13.620u 0.193s 0:14.07 98.1% 0+0k 0+0io 0pf+0w