Mon Oct 10 13:58:40 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 Mon Oct 10 2011 at 13:58:41 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: SEP 282 has a net charge of -0.4750 !!! WARNING: SEP 287 has a net charge of -0.4750 !!! WARNING: GLM 309 has a net charge of -0.0940 !!! WARNING: PRO 436 has a net charge of 0.5000 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: 0.6177553 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 0.6177553 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2623 net assigned charge : 2.470012 assigned positive charge : 426.0894 centred at (gu) : 89.41875 89.54230 90.17224 assigned negative charge : -423.6204 centred at (gu) : 89.40520 89.65009 90.00151 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7045 nv = 96 ne = 84 npr = 55349 no. pairs analyzed = 55349 no. exposed pairs = 3563 no. arc points = 25176 no. surface atoms = 1194 nbur = 1583 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3661 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.3700000 number of dielectric boundary points 3707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2614 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6305000E-09 1.3721451E-08 midg,1,midg; midg,igrid,midg 1.0031367E-08 -5.0434150E-09 1,midg,midg; igrid,midg,midg 1.0049469E-09 2.4133553E-09 gauss-seidel spectral radius is 0.9864496 estimated iterations to convergence 70 setup time was (sec) 0.6200000 now iterating at: 13:58:41 rms-change max change #iterations 0.1324404 22.78711 at 10iterations 1.1933384E-02 1.609318 at 20iterations 1.1010671E-03 0.1534944 at 30iterations 1.0112162E-04 2.1003723E-02 at 40iterations 9.7164202E-06 1.2846291E-03 at 50iterations finished qdiffx linear iterations at : 13:58:44 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 9.7164202E-06 1.2846291E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 13:58:45 3.603u 0.165s 0:04.15 90.6% 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 13:58:45 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: SEP 282 has a net charge of -0.4750 !!! WARNING: SEP 287 has a net charge of -0.4750 !!! WARNING: GLM 309 has a net charge of -0.0940 !!! WARNING: PRO 436 has a net charge of 0.5000 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: 1.853266 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 1.853266 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2623 net assigned charge : 2.470012 assigned positive charge : 426.0894 centred at (gu) : 88.25544 88.62614 90.51594 assigned negative charge : -423.6204 centred at (gu) : 88.21508 88.95002 90.00433 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25176 grid for indexing accessible points = 1.400000 m= 26497 mr = 51651 m= 3778 mr = 18726 m= 204 mr = 2139 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 815 time to turn everything in is 0.5800000 number of dielectric boundary points 34145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20525 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) : 0.6177553 object centre at (A) : 15.20300 -3.113000 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5007837E-03 1.6918218E-02 midg,1,midg; midg,igrid,midg 3.0448027E-02 1.1152111E-02 1,midg,midg; igrid,midg,midg -4.4632379E-02 -1.0688380E-02 gauss-seidel spectral radius is 0.9985885 estimated iterations to convergence 211 setup time was (sec) 0.9000000 now iterating at: 13:58:46 rms-change max change #iterations 4.259274 165.3171 at 10iterations 1.959964 66.36254 at 20iterations 0.9016658 30.20041 at 30iterations 0.4169831 12.72285 at 40iterations 0.1922679 5.906052 at 50iterations 8.9057207E-02 2.784215 at 60iterations 4.1002057E-02 1.307501 at 70iterations 1.8963400E-02 0.5806389 at 80iterations 8.7535148E-03 0.2799978 at 90iterations 4.0515587E-03 0.1245770 at 100iterations 1.8705907E-03 5.8210850E-02 at 110iterations 8.6551980E-04 2.7770996E-02 at 120iterations finished qdiffx linear iterations at : 13:58:53 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 8.6551980E-04 2.7770996E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 13:58:53 8.002u 0.207s 0:08.67 94.5% 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 13:58:53 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: HIR 136 has a net charge of 0.5140 !!! WARNING: SEP 282 has a net charge of -0.4750 !!! WARNING: SEP 287 has a net charge of -0.4750 !!! WARNING: GLM 309 has a net charge of -0.0940 !!! WARNING: PRO 436 has a net charge of 0.5000 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: 2.779899 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): -13.61100 44.01700 ymin,ymax (A): -28.60600 22.38000 zmin,zma (A): 21.26200 68.38500 x,y,z range (A): 57.62800 50.98600 47.12300 scale (grids/A): 2.779899 object centre (A): 15.20300 -3.113000 44.82350 number of atom coordinates read : 2777 total number of charged atoms : 2623 net assigned charge : 2.470012 assigned positive charge : 426.0894 centred at (gu) : 87.38287 87.93903 90.77392 assigned negative charge : -423.6204 centred at (gu) : 87.32261 88.42511 90.00636 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25176 grid for indexing accessible points = 1.400000 m= 87406 mr = 125652 m= 29569 mr = 70233 m= 6547 mr = 22928 m= 846 mr = 4567 m= 38 mr = 514 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 2699 time to turn everything in is 1.450000 number of dielectric boundary points 76882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 20973 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) : 1.853266 object centre at (A) : 15.20300 -3.113000 44.82350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8171541E-02 0.1161616 midg,1,midg; midg,igrid,midg 0.3531730 0.1329863 1,midg,midg; igrid,midg,midg -0.6615933 1.3753359E-02 gauss-seidel spectral radius is 0.9992531 estimated iterations to convergence 289 setup time was (sec) 1.780000 now iterating at: 13:58:55 rms-change max change #iterations 10.25206 285.3641 at 10iterations 6.050207 128.1084 at 20iterations 3.547843 96.24715 at 30iterations 2.061919 49.06464 at 40iterations 1.198154 24.83342 at 50iterations 0.6933340 12.82436 at 60iterations 0.4005613 9.023396 at 70iterations 0.2313167 4.116659 at 80iterations 0.1331599 2.408531 at 90iterations 7.6810576E-02 1.592501 at 100iterations 4.4062547E-02 0.7995949 at 110iterations 2.5344787E-02 0.4849586 at 120iterations 1.4591835E-02 0.3029480 at 130iterations 8.3811134E-03 0.1599197 at 140iterations 4.8129167E-03 8.4506989E-02 at 150iterations 2.7743841E-03 5.2543640E-02 at 160iterations 1.5952865E-03 3.1084061E-02 at 170iterations 9.2416641E-04 1.6942978E-02 at 180iterations finished qdiffx linear iterations at : 13:59:07 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 9.2416641E-04 1.6942978E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 13:59:07 13.082u 0.242s 0:13.79 96.5% 0+0k 0+0io 0pf+0w