Sat Oct 8 14:41:58 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 Sat Oct 8 2011 at 14:41:58 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6514181 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 0.6514181 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9859914 assigned positive charge : 448.7566 centred at (gu) : 89.16976 89.59948 90.98492 assigned negative charge : -449.7434 centred at (gu) : 89.16897 89.48582 90.93342 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8626 nv = 96 ne = 84 npr = 61744 no. pairs analyzed = 61744 no. exposed pairs = 3487 no. arc points = 24262 no. surface atoms = 1179 nbur = 1812 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 5087 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2306 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3050652E-09 9.1975965E-09 midg,1,midg; midg,igrid,midg -2.5124606E-08 1.7062662E-08 1,midg,midg; igrid,midg,midg -2.5109879E-09 -1.5467367E-09 gauss-seidel spectral radius is 0.9878200 estimated iterations to convergence 74 setup time was (sec) 0.6700000 now iterating at: 14:41:59 rms-change max change #iterations 0.1766087 22.70785 at 10iterations 1.8197076E-02 2.264868 at 20iterations 1.9460830E-03 0.2610378 at 30iterations 2.4020966E-04 3.3096313E-02 at 40iterations 4.0753072E-05 6.0119629E-03 at 50iterations finished qdiffx linear iterations at : 14:42:02 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 4.0753072E-05 6.0119629E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 14:42:03 4.252u 0.280s 0:04.80 94.3% 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 Sat Oct 8 2011 at 14:42:03 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.954254 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 1.954254 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9859914 assigned positive charge : 448.7566 centred at (gu) : 87.50863 88.79807 92.95430 assigned negative charge : -449.7434 centred at (gu) : 87.50655 88.45701 92.79990 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 94053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24262 grid for indexing accessible points = 1.400000 m= 35847 mr = 68374 m= 5920 mr = 27413 m= 372 mr = 3791 m= 2 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.9400000 number of dielectric boundary points 36487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 22455 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) : 0.6514181 object centre at (A) : 15.12200 -1.3500214E-02 21.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3685997E-02 2.0808218E-02 midg,1,midg; midg,igrid,midg -1.1604975E-02 1.8468274E-02 1,midg,midg; igrid,midg,midg -1.2916500E-02 1.0466988E-02 gauss-seidel spectral radius is 0.9987357 estimated iterations to convergence 223 setup time was (sec) 1.240000 now iterating at: 14:42:04 rms-change max change #iterations 4.890662 194.8919 at 10iterations 2.369149 75.33395 at 20iterations 1.140072 32.48494 at 30iterations 0.5530612 15.11517 at 40iterations 0.2662669 7.847954 at 50iterations 0.1281219 3.876829 at 60iterations 6.2076606E-02 1.659475 at 70iterations 3.0022573E-02 0.8362331 at 80iterations 1.4482848E-02 0.4210434 at 90iterations 7.0268386E-03 0.1912956 at 100iterations 3.3948235E-03 0.1076889 at 110iterations 1.6460286E-03 5.6104660E-02 at 120iterations finished qdiffx linear iterations at : 14:42:13 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 1.6460286E-03 5.6104660E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.18000 DelPhi exited at 14:42:13 10.182u 0.343s 0:10.80 97.4% 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 Sat Oct 8 2011 at 14:42:13 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2991 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.931381 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): -12.20300 42.44700 ymin,ymax (A): -22.29400 22.26700 zmin,zma (A): -6.122000 48.32500 x,y,z range (A): 54.65000 44.56100 54.44700 scale (grids/A): 2.931381 object centre (A): 15.12200 -1.3500214E-02 21.10150 number of atom coordinates read : 2991 total number of charged atoms : 2845 net assigned charge : -0.9859914 assigned positive charge : 448.7566 centred at (gu) : 86.26277 88.19688 94.43121 assigned negative charge : -449.7434 centred at (gu) : 86.25981 87.68548 94.19982 start vw surface at 0.1700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 217243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24262 grid for indexing accessible points = 1.400000 m= 115631 mr = 164758 m= 43351 mr = 96795 m= 10893 mr = 35645 m= 1626 mr = 8382 m= 102 mr = 1112 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 2.160000 number of dielectric boundary points 82122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 22760 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) : 1.954254 object centre at (A) : 15.12200 -1.3500214E-02 21.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1033869 0.3309525 midg,1,midg; midg,igrid,midg -7.7083990E-02 0.1957858 1,midg,midg; igrid,midg,midg -1.8381638E-02 0.3257940 gauss-seidel spectral radius is 0.9992886 estimated iterations to convergence 296 setup time was (sec) 2.500000 now iterating at: 14:42:16 rms-change max change #iterations 11.27746 453.2759 at 10iterations 6.650033 153.7217 at 20iterations 3.919688 77.33289 at 30iterations 2.297822 43.54592 at 40iterations 1.348256 24.05968 at 50iterations 0.7885842 13.44938 at 60iterations 0.4593132 7.576519 at 70iterations 0.2678832 4.637674 at 80iterations 0.1566373 2.678658 at 90iterations 9.0976410E-02 1.420990 at 100iterations 5.3027771E-02 0.9134407 at 110iterations 3.0876391E-02 0.4823570 at 120iterations 1.7962037E-02 0.2874651 at 130iterations 1.0454998E-02 0.1874542 at 140iterations 6.0836622E-03 0.1027374 at 150iterations 3.5441786E-03 5.5967331E-02 at 160iterations 2.0572823E-03 3.2485962E-02 at 170iterations 1.1970886E-03 1.9393921E-02 at 180iterations finished qdiffx linear iterations at : 14:42:31 total time elapsed so far: 17.16000 # loops : 180 mean,max change (kT/e) : 1.1970886E-03 1.9393921E-02 energy calculations done at 17.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.35000 DelPhi exited at 14:42:31 17.348u 0.361s 0:17.99 98.3% 0+0k 0+0io 0pf+0w