Mon Oct 10 14:00:09 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 14:00:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 600 has a net charge of 1.4000 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: 0.6174338 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 0.6174338 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.24940 88.99209 89.62321 assigned negative charge : -388.8955 centred at (gu) : 88.14977 89.05299 89.49866 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6347 nv = 96 ne = 84 npr = 53444 no. pairs analyzed = 53444 no. exposed pairs = 2976 no. arc points = 21667 no. surface atoms = 1006 nbur = 1567 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3507 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2900000 number of dielectric boundary points 3136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2188 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7157727E-09 1.0127678E-08 midg,1,midg; midg,igrid,midg 8.9656416E-09 -2.2158317E-10 1,midg,midg; igrid,midg,midg -4.1941477E-09 6.4857315E-09 gauss-seidel spectral radius is 0.9864109 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 14:00:10 rms-change max change #iterations 0.1246917 21.82214 at 10iterations 1.1215318E-02 1.527538 at 20iterations 1.0225287E-03 0.1501007 at 30iterations 9.6794975E-05 1.4122009E-02 at 40iterations 8.6487680E-06 1.2855530E-03 at 50iterations finished qdiffx linear iterations at : 14:00:12 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 8.6487680E-06 1.2855530E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:00:13 3.099u 0.133s 0:03.76 85.6% 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 14:00:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 600 has a net charge of 1.4000 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: 1.852301 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 1.852301 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.74758 86.97568 88.86920 assigned negative charge : -388.8955 centred at (gu) : 84.44905 87.15903 88.49565 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21667 grid for indexing accessible points = 1.400000 m= 23388 mr = 47794 m= 3330 mr = 17139 m= 154 mr = 1978 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4487 time to turn everything in is 0.4900000 number of dielectric boundary points 28974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19339 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) : 0.6174338 object centre at (A) : -6.537500 0.0000000E+00 16.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6125839E-02 3.0368892E-02 midg,1,midg; midg,igrid,midg 1.3516743E-02 5.0031848E-04 1,midg,midg; igrid,midg,midg -8.1182865E-04 3.1809814E-02 gauss-seidel spectral radius is 0.9985520 estimated iterations to convergence 208 setup time was (sec) 0.7600000 now iterating at: 14:00:14 rms-change max change #iterations 3.979199 168.5196 at 10iterations 1.819954 65.50356 at 20iterations 0.8324190 26.42025 at 30iterations 0.3813827 13.50167 at 40iterations 0.1741901 5.706406 at 50iterations 8.0211952E-02 2.620502 at 60iterations 3.6615364E-02 1.274117 at 70iterations 1.6785569E-02 0.5596313 at 80iterations 7.6772938E-03 0.2488289 at 90iterations 3.5343359E-03 0.1200924 at 100iterations 1.6145624E-03 5.0598145E-02 at 110iterations 7.3932158E-04 2.5904655E-02 at 120iterations finished qdiffx linear iterations at : 14:00:21 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 7.3932158E-04 2.5904655E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 14:00:22 7.511u 0.214s 0:08.90 86.7% 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 Mon Oct 10 2011 at 14:00:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 600 has a net charge of 1.4000 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: 2.778452 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): -31.26400 18.18900 ymin,ymax (A): -23.57600 23.57600 zmin,zma (A): -12.58100 45.07700 x,y,z range (A): 49.45300 47.15200 57.65800 scale (grids/A): 2.778452 object centre (A): -6.537500 0.0000000E+00 16.24800 number of atom coordinates read : 2573 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 82.12124 85.46337 88.30386 assigned negative charge : -388.8955 centred at (gu) : 81.67352 85.73847 87.74342 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 160164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21667 grid for indexing accessible points = 1.400000 m= 77890 mr = 116098 m= 26025 mr = 63772 m= 5797 mr = 20725 m= 693 mr = 4222 m= 36 mr = 435 m= 0 mr = 6 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 14849 time to turn everything in is 1.220000 number of dielectric boundary points 65347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19721 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) : 1.852301 object centre at (A) : -6.537500 0.0000000E+00 16.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0225321E-02 0.3870326 midg,1,midg; midg,igrid,midg 0.1616446 -1.4418514E-03 1,midg,midg; igrid,midg,midg 2.6111098E-03 0.3878570 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 14:00:24 rms-change max change #iterations 9.396233 295.2258 at 10iterations 5.388505 137.2475 at 20iterations 3.079323 73.14892 at 30iterations 1.755580 40.34900 at 40iterations 0.9985086 21.01947 at 50iterations 0.5682428 11.74991 at 60iterations 0.3227180 6.690542 at 70iterations 0.1837400 3.874637 at 80iterations 0.1043398 1.858456 at 90iterations 5.9326291E-02 1.206711 at 100iterations 3.3649482E-02 0.6548233 at 110iterations 1.9096430E-02 0.3744507 at 120iterations 1.0865142E-02 0.2461262 at 130iterations 6.1703511E-03 0.1173573 at 140iterations 3.5060169E-03 6.9118500E-02 at 150iterations 1.9930180E-03 3.8314819E-02 at 160iterations 1.1307832E-03 2.2079468E-02 at 170iterations 6.4507563E-04 1.3504028E-02 at 180iterations finished qdiffx linear iterations at : 14:00:34 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 6.4507563E-04 1.3504028E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 14:00:36 12.205u 0.240s 0:13.44 92.5% 0+0k 0+0io 0pf+0w