Sun Oct 9 16:58:04 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 Sun Oct 9 2011 at 16:58:04 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 = 5043 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: 0.5156804 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 0.5156804 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4887 net assigned charge : 11.00005 assigned positive charge : 763.1752 centred at (gu) : 89.85579 90.52522 90.29305 assigned negative charge : -752.1810 centred at (gu) : 89.92691 90.62357 90.14587 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8284 nv = 96 ne = 84 npr = 103749 no. pairs analyzed = 103749 no. exposed pairs = 5908 no. arc points = 40425 no. surface atoms = 2004 nbur = 3039 mkacc time = 0.2300000 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 = 1.680000 m= 281 mr = 4480 m= 0 mr = 4 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4800000 number of dielectric boundary points 4081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4130 ## 632 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 11360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8872985E-10 7.4003670E-10 midg,1,midg; midg,igrid,midg 4.5805174E-10 -1.6442819E-10 1,midg,midg; igrid,midg,midg 4.5146953E-10 -4.5243705E-11 gauss-seidel spectral radius is 0.9807771 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 16:58:05 rms-change max change #iterations 7.6277584E-02 13.98227 at 10iterations 5.9348373E-03 0.7620068 at 20iterations 1.4596639E-03 0.2497444 at 30iterations 5.9394212E-04 0.1033230 at 40iterations 2.4865250E-04 4.3695450E-02 at 50iterations finished qdiffx linear iterations at : 16:58:07 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.4865250E-04 4.3695450E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 16:58:08 3.292u 0.141s 0:03.71 92.4% 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 16:58:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 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: 1.547041 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 1.547041 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4887 net assigned charge : 11.00005 assigned positive charge : 763.1752 centred at (gu) : 89.56541 91.57423 90.87747 assigned negative charge : -752.1810 centred at (gu) : 89.78041 91.87043 90.43746 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 94987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26796 mr = 67147 m= 2286 mr = 18072 m= 45 mr = 978 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 336 time to turn everything in is 0.6300000 number of dielectric boundary points 37917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 615 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 36831 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) : 0.5156804 object centre at (A) : 34.69550 26.62000 -1.659500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8646756E-02 3.8802907E-02 midg,1,midg; midg,igrid,midg 1.5987892E-02 -2.5398161E-03 1,midg,midg; igrid,midg,midg 2.2490891E-02 8.5213259E-03 gauss-seidel spectral radius is 0.9981660 estimated iterations to convergence 186 setup time was (sec) 0.9000000 now iterating at: 16:58:09 rms-change max change #iterations 3.972436 156.1009 at 10iterations 1.643881 50.28021 at 20iterations 0.6864431 20.72168 at 30iterations 0.2855370 8.349827 at 40iterations 0.1188859 3.760860 at 50iterations 4.9775280E-02 1.491100 at 60iterations 2.0972801E-02 0.7098808 at 70iterations 9.1073299E-03 0.3278008 at 80iterations 4.2223651E-03 0.1498413 at 90iterations 2.2222591E-03 7.6309204E-02 at 100iterations 1.3491978E-03 4.9102783E-02 at 110iterations 9.1008149E-04 3.2844543E-02 at 120iterations finished qdiffx linear iterations at : 16:58:15 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 9.1008149E-04 3.2844543E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 16:58:16 7.274u 0.169s 0:07.70 96.4% 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 16:58:16 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 = 5043 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.320562 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): 3.122000 66.26900 ymin,ymax (A): -0.9190000 54.15900 zmin,zma (A): -36.17700 32.85800 x,y,z range (A): 63.14700 55.07800 69.03500 scale (grids/A): 2.320562 object centre (A): 34.69550 26.62000 -1.659500 number of atom coordinates read : 5043 total number of charged atoms : 4887 net assigned charge : 11.00005 assigned positive charge : 763.1752 centred at (gu) : 89.34774 92.36078 91.31580 assigned negative charge : -752.1810 centred at (gu) : 89.67061 92.80534 90.65623 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 222299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40425 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 97275 mr = 164901 m= 23815 mr = 76767 m= 3189 mr = 17260 m= 149 mr = 2012 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1141 time to turn everything in is 1.490000 number of dielectric boundary points 85750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 39007 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) : 1.547041 object centre at (A) : 34.69550 26.62000 -1.659500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4382528 0.6157193 midg,1,midg; midg,igrid,midg 0.2269342 -5.1997967E-02 1,midg,midg; igrid,midg,midg 0.3613176 0.2170417 gauss-seidel spectral radius is 0.9991790 estimated iterations to convergence 276 setup time was (sec) 1.770000 now iterating at: 16:58:17 rms-change max change #iterations 10.75514 286.0098 at 10iterations 6.225428 153.1749 at 20iterations 3.573298 76.20942 at 30iterations 2.037983 49.55215 at 40iterations 1.158009 23.94058 at 50iterations 0.6533694 12.64954 at 60iterations 0.3693703 7.238102 at 70iterations 0.2075374 4.193787 at 80iterations 0.1168926 2.299221 at 90iterations 6.5714724E-02 1.168898 at 100iterations 3.6876854E-02 0.6953559 at 110iterations 2.0707477E-02 0.3828020 at 120iterations 1.1604860E-02 0.2125165 at 130iterations 6.5256720E-03 0.1219034 at 140iterations 3.6785908E-03 6.5429688E-02 at 150iterations 2.0862056E-03 4.3048859E-02 at 160iterations 1.1964447E-03 2.2786140E-02 at 170iterations 7.0676528E-04 1.4953613E-02 at 180iterations finished qdiffx linear iterations at : 16:58:27 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 7.0676528E-04 1.4953613E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 16:58:28 11.722u 0.162s 0:12.15 97.7% 0+0k 0+0io 0pf+0w