Wed Feb 15 08:54:50 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:51 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 = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6071873 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 0.6071873 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.04376 91.80029 91.10492 assigned negative charge : -392.8965 centred at (gu) : 89.91251 91.72071 90.99491 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6299 nv = 96 ne = 84 npr = 52274 no. pairs analyzed = 52274 no. exposed pairs = 3565 no. arc points = 25283 no. surface atoms = 1192 nbur = 1398 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3114 m= 0 mr = 26 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2100000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2462 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6729423E-09 4.3983409E-10 midg,1,midg; midg,igrid,midg -5.6389466E-09 -1.4948541E-09 1,midg,midg; igrid,midg,midg -1.0700336E-08 1.2437985E-09 gauss-seidel spectral radius is 0.9859646 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 08:54:51 rms-change max change #iterations 0.1118295 17.67964 at 10iterations 9.7917533E-03 1.563470 at 20iterations 8.5372926E-04 0.1580060 at 30iterations 8.1250910E-05 1.2273788E-02 at 40iterations 8.9124260E-06 1.5974045E-03 at 50iterations finished qdiffx linear iterations at : 08:54:55 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 8.9124260E-06 1.5974045E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 08:54:56 4.280u 0.378s 0:05.87 79.2% 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 Wed Feb 15 2012 at 08:54:56 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 = 2590 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: 1.821562 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 1.821562 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.13032 95.40025 93.31398 assigned negative charge : -392.8965 centred at (gu) : 89.73734 95.16183 92.98457 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25283 grid for indexing accessible points = 1.400000 m= 22415 mr = 44920 m= 3108 mr = 15234 m= 159 mr = 1713 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 568 time to turn everything in is 0.3500000 number of dielectric boundary points 32340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19142 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) : 0.6071873 object centre at (A) : 9.826501 -2.395000 15.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5858853E-02 -2.0867614E-02 midg,1,midg; midg,igrid,midg -1.1446015E-02 -8.5819392E-03 1,midg,midg; igrid,midg,midg 1.0453227E-03 -1.2184335E-02 gauss-seidel spectral radius is 0.9985201 estimated iterations to convergence 206 setup time was (sec) 0.5900000 now iterating at: 08:54:57 rms-change max change #iterations 3.891135 212.8904 at 10iterations 1.758605 62.88379 at 20iterations 0.7935355 26.04284 at 30iterations 0.3599212 11.53719 at 40iterations 0.1631775 5.975208 at 50iterations 7.3724285E-02 2.650915 at 60iterations 3.3492256E-02 1.093195 at 70iterations 1.5111917E-02 0.5186996 at 80iterations 6.8555996E-03 0.2424011 at 90iterations 3.1116288E-03 0.1011963 at 100iterations 1.4153454E-03 5.2876949E-02 at 110iterations 6.4207619E-04 2.1127701E-02 at 120iterations finished qdiffx linear iterations at : 08:55:05 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 6.4207619E-04 2.1127701E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 08:55:06 8.675u 0.267s 0:09.31 95.9% 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 Wed Feb 15 2012 at 08:55:06 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 = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.732343 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): -19.48900 39.14200 ymin,ymax (A): -26.37000 21.58000 zmin,zma (A): -12.04400 42.95400 x,y,z range (A): 58.63100 47.95000 54.99800 scale (grids/A): 2.732343 object centre (A): 9.826501 -2.395000 15.45500 number of atom coordinates read : 2590 total number of charged atoms : 2440 net assigned charge : -8.499987 assigned positive charge : 384.3955 centred at (gu) : 90.19524 98.09993 94.97083 assigned negative charge : -392.8965 centred at (gu) : 89.60598 97.74268 94.47684 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 158740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25283 grid for indexing accessible points = 1.400000 m= 74215 mr = 110204 m= 24488 mr = 57962 m= 5366 mr = 18369 m= 666 mr = 3676 m= 22 mr = 362 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1897 time to turn everything in is 0.9100000 number of dielectric boundary points 72922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19518 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) : 1.821562 object centre at (A) : 9.826501 -2.395000 15.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7143105E-02 -0.3549782 midg,1,midg; midg,igrid,midg -9.7588874E-02 -0.1085749 1,midg,midg; igrid,midg,midg 0.4952215 -0.1655895 gauss-seidel spectral radius is 0.9992371 estimated iterations to convergence 286 setup time was (sec) 1.180000 now iterating at: 08:55:07 rms-change max change #iterations 9.497283 294.8010 at 10iterations 5.551421 125.9194 at 20iterations 3.216205 65.80654 at 30iterations 1.849748 41.29852 at 40iterations 1.064459 21.08337 at 50iterations 0.6085849 13.51277 at 60iterations 0.3485034 7.772819 at 70iterations 0.1987869 4.304116 at 80iterations 0.1135174 2.277679 at 90iterations 6.4750284E-02 1.312399 at 100iterations 3.6892146E-02 0.7362576 at 110iterations 2.1007355E-02 0.4362183 at 120iterations 1.1976080E-02 0.2499580 at 130iterations 6.8171294E-03 0.1429710 at 140iterations 3.8837662E-03 7.5362206E-02 at 150iterations 2.2150285E-03 4.0076017E-02 at 160iterations 1.2600652E-03 2.4810791E-02 at 170iterations 7.2215992E-04 1.4358521E-02 at 180iterations finished qdiffx linear iterations at : 08:55:19 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 7.2215992E-04 1.4358521E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:55:19 12.941u 0.280s 0:13.59 97.2% 0+0k 0+0io 0pf+0w