Mon Oct 10 10:24:19 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+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 10:24:19 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2812 !!! WARNING: HIT 228 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5825274 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): -17.74000 33.73800 ymin,ymax (A): -59.73900 -0.6720001 zmin,zma (A): -1.637000 59.47600 x,y,z range (A): 51.47800 59.06700 61.11300 scale (grids/A): 0.5825274 object centre (A): 7.999000 -30.20550 28.91950 number of atom coordinates read : 2812 total number of charged atoms : 2661 net assigned charge : 6.014015 assigned positive charge : 415.3769 centred at (gu) : 88.41478 88.31540 88.14209 assigned negative charge : -409.3633 centred at (gu) : 88.48554 88.19781 88.04461 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6490 nv = 96 ne = 84 npr = 54756 no. pairs analyzed = 54756 no. exposed pairs = 4170 no. arc points = 30485 no. surface atoms = 1386 nbur = 1426 mkacc time = 0.1300000 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 = 1.484000 m= 332 mr = 2840 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3001 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8063 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0813890E-09 2.3396338E-09 midg,1,midg; midg,igrid,midg -1.7061322E-09 2.7214719E-09 1,midg,midg; igrid,midg,midg 4.3727204E-09 -2.7456114E-11 gauss-seidel spectral radius is 0.9847947 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 10:24:20 rms-change max change #iterations 9.9367462E-02 15.82308 at 10iterations 7.6796189E-03 1.264902 at 20iterations 5.9985719E-04 9.6927643E-02 at 30iterations 5.1405816E-05 7.8306198E-03 at 40iterations 5.4372176E-06 7.5018406E-04 at 50iterations finished qdiffx linear iterations at : 10:24:23 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 5.4372176E-06 7.5018406E-04 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 10:24:23 3.636u 0.197s 0:04.20 90.9% 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 10:24:23 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2812 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 1.747582 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): -17.74000 33.73800 ymin,ymax (A): -59.73900 -0.6720001 zmin,zma (A): -1.637000 59.47600 x,y,z range (A): 51.47800 59.06700 61.11300 scale (grids/A): 1.747582 object centre (A): 7.999000 -30.20550 28.91950 number of atom coordinates read : 2812 total number of charged atoms : 2661 net assigned charge : 6.014015 assigned positive charge : 415.3769 centred at (gu) : 85.24375 84.94555 84.42569 assigned negative charge : -409.3633 centred at (gu) : 85.45641 84.59322 84.13335 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30485 grid for indexing accessible points = 1.400000 m= 21836 mr = 42428 m= 2721 mr = 13834 m= 117 mr = 1168 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20713 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) : 0.5825274 object centre at (A) : 7.999000 -30.20550 28.91950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2470646E-03 9.8059988E-03 midg,1,midg; midg,igrid,midg 1.7366473E-02 3.0016754E-02 1,midg,midg; igrid,midg,midg 9.2913276E-03 5.5518020E-03 gauss-seidel spectral radius is 0.9984277 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 10:24:25 rms-change max change #iterations 3.731127 172.2955 at 10iterations 1.642058 62.30494 at 20iterations 0.7241757 27.67390 at 30iterations 0.3199140 11.28667 at 40iterations 0.1406686 5.314072 at 50iterations 6.2455107E-02 2.012151 at 60iterations 2.7576484E-02 1.086654 at 70iterations 1.2158882E-02 0.4086142 at 80iterations 5.3852154E-03 0.2034912 at 90iterations 2.3739992E-03 7.6538086E-02 at 100iterations 1.0535578E-03 3.4086227E-02 at 110iterations 4.6448788E-04 1.7738342E-02 at 120iterations finished qdiffx linear iterations at : 10:24:32 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 4.6448788E-04 1.7738342E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 10:24:32 8.148u 0.214s 0:08.71 95.8% 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 10:24:32 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2812 !!! WARNING: HIT 228 has a net charge of 0.5140 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: 2.621373 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): -17.74000 33.73800 ymin,ymax (A): -59.73900 -0.6720001 zmin,zma (A): -1.637000 59.47600 x,y,z range (A): 51.47800 59.06700 61.11300 scale (grids/A): 2.621373 object centre (A): 7.999000 -30.20550 28.91950 number of atom coordinates read : 2812 total number of charged atoms : 2661 net assigned charge : 6.014015 assigned positive charge : 415.3769 centred at (gu) : 82.86563 82.41815 81.63847 assigned negative charge : -409.3633 centred at (gu) : 83.18456 81.88985 81.19991 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 160222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30485 grid for indexing accessible points = 1.400000 m= 72001 mr = 104712 m= 22807 mr = 53645 m= 4325 mr = 16142 m= 423 mr = 2590 m= 9 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 82528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 21282 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) : 1.747582 object centre at (A) : 7.999000 -30.20550 28.91950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1214070 6.5760620E-02 midg,1,midg; midg,igrid,midg 0.3459541 0.4083016 1,midg,midg; igrid,midg,midg 5.4100338E-02 8.0152065E-02 gauss-seidel spectral radius is 0.9992273 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 10:24:34 rms-change max change #iterations 9.477416 273.0626 at 10iterations 5.590483 147.0502 at 20iterations 3.246217 91.19060 at 30iterations 1.881579 47.50051 at 40iterations 1.085850 24.72106 at 50iterations 0.6223795 13.09611 at 60iterations 0.3562796 7.731781 at 70iterations 0.2040781 3.995190 at 80iterations 0.1159845 2.582997 at 90iterations 6.6379532E-02 1.458662 at 100iterations 3.7769724E-02 0.8337989 at 110iterations 2.1486163E-02 0.4734244 at 120iterations 1.2212054E-02 0.2392464 at 130iterations 6.9504292E-03 0.1515827 at 140iterations 3.9470796E-03 7.8830719E-02 at 150iterations 2.2404399E-03 4.6621680E-02 at 160iterations 1.2679310E-03 2.4879456E-02 at 170iterations 7.2081783E-04 1.5547752E-02 at 180iterations finished qdiffx linear iterations at : 10:24:46 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 7.2081783E-04 1.5547752E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 10:24:46 13.296u 0.224s 0:13.95 96.8% 0+0k 0+0io 0pf+0w