Sun Oct 9 21:53:07 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 21:53:08 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 = 3155 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: 0.6582110 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): 45.39500 98.43200 ymin,ymax (A): 2.992000 57.07800 zmin,zma (A): 15.15800 67.99700 x,y,z range (A): 53.03700 54.08600 52.83900 scale (grids/A): 0.6582110 object centre (A): 71.91350 30.03500 41.57750 number of atom coordinates read : 3155 total number of charged atoms : 3007 net assigned charge : 4.500013 assigned positive charge : 478.7608 centred at (gu) : 90.60713 88.53561 90.60262 assigned negative charge : -474.2621 centred at (gu) : 90.48022 88.48885 90.61764 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9312 nv = 96 ne = 84 npr = 62019 no. pairs analyzed = 62019 no. exposed pairs = 4101 no. arc points = 29507 no. surface atoms = 1375 nbur = 1780 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4929 m= 6 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3500000 number of dielectric boundary points 4853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2864 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10999 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2689009E-08 8.3586835E-09 midg,1,midg; midg,igrid,midg -1.6737617E-10 1.5998371E-08 1,midg,midg; igrid,midg,midg -1.6399179E-08 4.5135248E-08 gauss-seidel spectral radius is 0.9880977 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 21:53:08 rms-change max change #iterations 0.1839880 21.39068 at 10iterations 1.9258080E-02 2.420525 at 20iterations 2.0692800E-03 0.2407455 at 30iterations 2.2058080E-04 2.9745102E-02 at 40iterations 2.3601784E-05 2.7160645E-03 at 50iterations finished qdiffx linear iterations at : 21:53:12 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 2.3601784E-05 2.7160645E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 21:53:13 4.500u 0.404s 0:05.20 94.2% 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 Sun Oct 9 2011 at 21:53:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3155 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: 1.974633 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): 45.39500 98.43200 ymin,ymax (A): 2.992000 57.07800 zmin,zma (A): 15.15800 67.99700 x,y,z range (A): 53.03700 54.08600 52.83900 scale (grids/A): 1.974633 object centre (A): 71.91350 30.03500 41.57750 number of atom coordinates read : 3155 total number of charged atoms : 3007 net assigned charge : 4.500013 assigned positive charge : 478.7608 centred at (gu) : 91.82040 85.60595 91.80677 assigned negative charge : -474.2621 centred at (gu) : 91.44029 85.46616 91.85274 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 100511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29507 grid for indexing accessible points = 1.400000 m= 35676 mr = 68699 m= 5847 mr = 25580 m= 433 mr = 3479 m= 7 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2722 time to turn everything in is 0.8000000 number of dielectric boundary points 44577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 23751 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) : 0.6582110 object centre at (A) : 71.91350 30.03500 41.57750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3967108E-03 -1.9864751E-02 midg,1,midg; midg,igrid,midg 5.2663285E-02 3.4821045E-02 1,midg,midg; igrid,midg,midg -5.5246907E-03 3.4279633E-02 gauss-seidel spectral radius is 0.9987893 estimated iterations to convergence 228 setup time was (sec) 1.120000 now iterating at: 21:53:14 rms-change max change #iterations 5.052019 189.7615 at 10iterations 2.464374 77.92235 at 20iterations 1.201387 32.53123 at 30iterations 0.5880643 18.23677 at 40iterations 0.2872316 7.813801 at 50iterations 0.1404223 3.833145 at 60iterations 6.8558045E-02 2.013072 at 70iterations 3.3598319E-02 1.051736 at 80iterations 1.6428528E-02 0.4721117 at 90iterations 8.0192294E-03 0.2385988 at 100iterations 3.9193239E-03 0.1074733 at 110iterations 1.9186641E-03 5.1425297E-02 at 120iterations finished qdiffx linear iterations at : 21:53:25 total time elapsed so far: 12.08000 # loops : 120 mean,max change (kT/e) : 1.9186641E-03 5.1425297E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 21:53:26 12.253u 0.452s 0:12.96 97.9% 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 Sun Oct 9 2011 at 21:53:26 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 = 3155 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: 2.961949 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): 45.39500 98.43200 ymin,ymax (A): 2.992000 57.07800 zmin,zma (A): 15.15800 67.99700 x,y,z range (A): 53.03700 54.08600 52.83900 scale (grids/A): 2.961949 object centre (A): 71.91350 30.03500 41.57750 number of atom coordinates read : 3155 total number of charged atoms : 3007 net assigned charge : 4.500013 assigned positive charge : 478.7608 centred at (gu) : 92.73029 83.40897 92.71004 assigned negative charge : -474.2621 centred at (gu) : 92.16035 83.19919 92.77901 start vw surface at 0.1400000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 232632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29507 grid for indexing accessible points = 1.400000 m= 115616 mr = 167127 m= 41588 mr = 93332 m= 10440 mr = 32342 m= 1645 mr = 7534 m= 122 mr = 992 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 9126 time to turn everything in is 2.140000 number of dielectric boundary points 100660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 24056 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) : 1.974633 object centre at (A) : 71.91350 30.03500 41.57750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8722524E-02 -0.3911896 midg,1,midg; midg,igrid,midg 0.3276708 0.3202324 1,midg,midg; igrid,midg,midg 9.9431887E-02 0.4737029 gauss-seidel spectral radius is 0.9993187 estimated iterations to convergence 302 setup time was (sec) 2.490000 now iterating at: 21:53:29 rms-change max change #iterations 11.84261 519.8341 at 10iterations 7.145903 221.0552 at 20iterations 4.273754 86.88241 at 30iterations 2.559569 51.85158 at 40iterations 1.525785 27.67064 at 50iterations 0.9060670 17.18224 at 60iterations 0.5358361 9.040417 at 70iterations 0.3178951 5.285925 at 80iterations 0.1879314 3.184397 at 90iterations 0.1108349 1.789808 at 100iterations 6.5489233E-02 1.119821 at 110iterations 3.8673021E-02 0.6177263 at 120iterations 2.2779683E-02 0.3735378 at 130iterations 1.3429814E-02 0.2164726 at 140iterations 7.9163713E-03 0.1260300 at 150iterations 4.6592848E-03 7.0789337E-02 at 160iterations 2.7461911E-03 4.4715881E-02 at 170iterations 1.6176591E-03 2.6375771E-02 at 180iterations finished qdiffx linear iterations at : 21:53:46 total time elapsed so far: 19.84000 # loops : 180 mean,max change (kT/e) : 1.6176591E-03 2.6375771E-02 energy calculations done at 19.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.00000 DelPhi exited at 21:53:47 20.008u 0.492s 0:20.81 98.4% 0+0k 0+0io 0pf+0w