Mon Oct 10 09:44:19 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 09:44:19 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 = 2842 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: 0.5649986 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 0.5649986 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.000015 assigned positive charge : 415.3578 centred at (gu) : 89.45866 88.94632 89.48263 assigned negative charge : -408.3583 centred at (gu) : 89.54462 89.07246 89.30006 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5977 nv = 96 ne = 84 npr = 55730 no. pairs analyzed = 55730 no. exposed pairs = 4274 no. arc points = 31210 no. surface atoms = 1408 nbur = 1434 mkacc time = 0.1200000 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 = 1.512000 m= 314 mr = 2583 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3016 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5699749E-09 2.6954947E-09 midg,1,midg; midg,igrid,midg 3.0849923E-09 -5.0763505E-10 1,midg,midg; igrid,midg,midg 2.1832636E-09 -1.4122888E-10 gauss-seidel spectral radius is 0.9838421 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 09:44:19 rms-change max change #iterations 8.2482584E-02 14.33484 at 10iterations 5.8729770E-03 0.9807816 at 20iterations 4.1588940E-04 6.6753387E-02 at 30iterations 3.4797642E-05 5.1116943E-03 at 40iterations 4.0246068E-06 5.9890747E-04 at 50iterations finished qdiffx linear iterations at : 09:44:22 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 4.0246068E-06 5.9890747E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 09:44:22 3.191u 0.132s 0:03.61 91.9% 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 Mon Oct 10 2011 at 09:44:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2842 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: 1.694996 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 1.694996 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.000015 assigned positive charge : 415.3578 centred at (gu) : 88.37547 86.83836 88.44733 assigned negative charge : -408.3583 centred at (gu) : 88.63335 87.21725 87.89985 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31210 grid for indexing accessible points = 1.400000 m= 20161 mr = 38331 m= 2546 mr = 12595 m= 100 mr = 1138 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 34360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 20792 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) : 0.5649986 object centre at (A) : 144.0775 -16.09000 74.51801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1661329E-02 2.0422289E-02 midg,1,midg; midg,igrid,midg 1.8851366E-02 3.8437874E-03 1,midg,midg; igrid,midg,midg 1.3825772E-02 7.1492507E-03 gauss-seidel spectral radius is 0.9983296 estimated iterations to convergence 194 setup time was (sec) 0.7400000 now iterating at: 09:44:23 rms-change max change #iterations 3.416347 185.2764 at 10iterations 1.468196 60.05029 at 20iterations 0.6311905 23.93264 at 30iterations 0.2728271 10.01828 at 40iterations 0.1170333 4.660163 at 50iterations 5.0442368E-02 1.772003 at 60iterations 2.1717593E-02 0.8007507 at 70iterations 9.3714502E-03 0.3551435 at 80iterations 4.0240572E-03 0.1419191 at 90iterations 1.7400648E-03 6.7745209E-02 at 100iterations 7.5168366E-04 2.7456284E-02 at 110iterations 3.2327697E-04 1.2954712E-02 at 120iterations finished qdiffx linear iterations at : 09:44:29 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 3.2327697E-04 1.2954712E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 09:44:30 7.023u 0.167s 0:07.48 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 Mon Oct 10 2011 at 09:44:30 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 = 2842 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: 2.542494 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 2.542494 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.000015 assigned positive charge : 415.3578 centred at (gu) : 87.56302 85.25742 87.67090 assigned negative charge : -408.3583 centred at (gu) : 87.94994 85.82585 86.84972 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 146946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31210 grid for indexing accessible points = 1.400000 m= 65532 mr = 94680 m= 21213 mr = 48412 m= 4020 mr = 14971 m= 333 mr = 2334 m= 20 mr = 137 m= 0 mr = 6 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 77524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21530 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) : 1.694996 object centre at (A) : 144.0775 -16.09000 74.51801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1375152 0.2689755 midg,1,midg; midg,igrid,midg 0.2710972 8.2312480E-02 1,midg,midg; igrid,midg,midg 0.2215066 6.6801287E-02 gauss-seidel spectral radius is 0.9991987 estimated iterations to convergence 279 setup time was (sec) 1.390000 now iterating at: 09:44:32 rms-change max change #iterations 8.924397 331.0005 at 10iterations 5.224681 174.7693 at 20iterations 3.016144 76.36780 at 30iterations 1.727245 42.37216 at 40iterations 0.9816703 22.16976 at 50iterations 0.5590069 13.85157 at 60iterations 0.3159065 8.559538 at 70iterations 0.1784967 3.976419 at 80iterations 0.1008462 2.204802 at 90iterations 5.6834728E-02 1.275762 at 100iterations 3.1986170E-02 0.6854342 at 110iterations 1.8006912E-02 0.3582714 at 120iterations 1.0104606E-02 0.2173414 at 130iterations 5.6707589E-03 0.1163502 at 140iterations 3.1910904E-03 7.3316574E-02 at 150iterations 1.7884873E-03 3.9529800E-02 at 160iterations 1.0050382E-03 2.1408081E-02 at 170iterations 5.6357833E-04 1.2390137E-02 at 180iterations finished qdiffx linear iterations at : 09:44:41 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 5.6357833E-04 1.2390137E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 09:44:42 11.250u 0.207s 0:12.43 92.1% 0+0k 0+0io 0pf+0w