Tue Oct 11 03:44:27 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 Tue Oct 11 2011 at 03:44:28 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIR 79 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6737575 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 0.6737575 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.514015 assigned positive charge : 411.0569 centred at (gu) : 89.97182 89.95071 90.96717 assigned negative charge : -406.5434 centred at (gu) : 89.71740 89.76579 90.94221 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8291 nv = 96 ne = 84 npr = 54941 no. pairs analyzed = 54941 no. exposed pairs = 3277 no. arc points = 22540 no. surface atoms = 1091 nbur = 1608 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4826 m= 4 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3300000 number of dielectric boundary points 3888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2094 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7889482E-09 2.9090875E-08 midg,1,midg; midg,igrid,midg -3.8918476E-08 6.9025369E-08 1,midg,midg; igrid,midg,midg -6.0158214E-08 8.8636469E-08 gauss-seidel spectral radius is 0.9885865 estimated iterations to convergence 76 setup time was (sec) 0.6200000 now iterating at: 03:44:29 rms-change max change #iterations 0.1889305 25.11488 at 10iterations 2.1158665E-02 2.708366 at 20iterations 2.3920380E-03 0.3182583 at 30iterations 2.7560748E-04 3.5238266E-02 at 40iterations 3.4218661E-05 4.1685104E-03 at 50iterations finished qdiffx linear iterations at : 03:44:33 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 3.4218661E-05 4.1685104E-03 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 03:44:33 5.059u 0.441s 0:05.92 92.7% 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 Tue Oct 11 2011 at 03:44:33 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIR 79 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.021272 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 2.021272 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.514015 assigned positive charge : 411.0569 centred at (gu) : 89.91506 89.85155 92.90083 assigned negative charge : -406.5434 centred at (gu) : 89.15190 89.29711 92.82625 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22540 grid for indexing accessible points = 1.400000 m= 36021 mr = 63140 m= 6855 mr = 27759 m= 531 mr = 4609 m= 7 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2393 time to turn everything in is 0.7500000 number of dielectric boundary points 36078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20196 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) : 0.6737575 object centre at (A) : 13.33450 -2.489000 19.42100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5415677E-02 3.9608423E-03 midg,1,midg; midg,igrid,midg -1.2292685E-02 5.5589594E-02 1,midg,midg; igrid,midg,midg -1.2288872E-02 8.5440323E-02 gauss-seidel spectral radius is 0.9987895 estimated iterations to convergence 228 setup time was (sec) 1.100000 now iterating at: 03:44:35 rms-change max change #iterations 4.932912 232.8349 at 10iterations 2.423445 93.91104 at 20iterations 1.186267 33.35052 at 30iterations 0.5821673 16.42781 at 40iterations 0.2856089 7.830576 at 50iterations 0.1405002 4.325069 at 60iterations 6.8790644E-02 1.941137 at 70iterations 3.3844292E-02 1.044645 at 80iterations 1.6595731E-02 0.5113831 at 90iterations 8.1417253E-03 0.2313118 at 100iterations 4.0005851E-03 0.1086121 at 110iterations 1.9665335E-03 5.9123993E-02 at 120iterations finished qdiffx linear iterations at : 03:44:46 total time elapsed so far: 12.29000 # loops : 120 mean,max change (kT/e) : 1.9665335E-03 5.9123993E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 03:44:47 12.467u 0.494s 0:13.25 97.7% 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 Tue Oct 11 2011 at 03:44:47 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIR 79 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.031909 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): -10.71200 37.38100 ymin,ymax (A): -26.63900 21.66100 zmin,zma (A): -6.998000 45.84000 x,y,z range (A): 48.09300 48.30000 52.83800 scale (grids/A): 3.031909 object centre (A): 13.33450 -2.489000 19.42100 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 4.514015 assigned positive charge : 411.0569 centred at (gu) : 89.87238 89.77702 94.35141 assigned negative charge : -406.5434 centred at (gu) : 88.72784 88.94569 94.23929 start vw surface at 0.1200000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 203914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22540 grid for indexing accessible points = 1.400000 m= 112241 mr = 152163 m= 46052 mr = 93923 m= 12780 mr = 38243 m= 2322 mr = 10026 m= 241 mr = 1757 m= 4 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 8700 time to turn everything in is 2.040000 number of dielectric boundary points 81295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 20416 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) : 2.021272 object centre at (A) : 13.33450 -2.489000 19.42100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2997349 0.2567044 midg,1,midg; midg,igrid,midg -0.1385174 0.5843678 1,midg,midg; igrid,midg,midg -2.7529625E-02 0.7179922 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 2.420000 now iterating at: 03:44:50 rms-change max change #iterations 11.16253 470.6691 at 10iterations 6.599939 139.8000 at 20iterations 3.884413 78.42892 at 30iterations 2.285355 41.80097 at 40iterations 1.341841 23.23926 at 50iterations 0.7855446 14.76697 at 60iterations 0.4607139 8.370373 at 70iterations 0.2704361 4.690381 at 80iterations 0.1582596 3.038607 at 90iterations 9.2467971E-02 1.640298 at 100iterations 5.4184634E-02 0.8885956 at 110iterations 3.1617958E-02 0.5035915 at 120iterations 1.8495699E-02 0.2942734 at 130iterations 1.0843175E-02 0.1809144 at 140iterations 6.3566905E-03 0.1101894 at 150iterations 3.7369835E-03 5.9778333E-02 at 160iterations 2.2118753E-03 3.4555435E-02 at 170iterations 1.3139169E-03 2.2907257E-02 at 180iterations finished qdiffx linear iterations at : 03:45:08 total time elapsed so far: 21.10000 # loops : 180 mean,max change (kT/e) : 1.3139169E-03 2.2907257E-02 energy calculations done at 21.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.27000 DelPhi exited at 03:45:09 21.274u 0.526s 0:22.40 97.2% 0+0k 0+0io 0pf+0w