Tue Oct 11 08:15:38 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 Tue Oct 11 2011 at 08:15:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6820708 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 0.6820708 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 425.2113 centred at (gu) : 90.98122 90.00215 89.35152 assigned negative charge : -420.2124 centred at (gu) : 90.73067 89.97088 89.31169 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8682 nv = 96 ne = 84 npr = 57048 no. pairs analyzed = 57048 no. exposed pairs = 3395 no. arc points = 22946 no. surface atoms = 1134 nbur = 1626 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 5001 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2100000 number of dielectric boundary points 4116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2181 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8663183E-09 3.2127303E-08 midg,1,midg; midg,igrid,midg 1.0239202E-08 3.3404884E-08 1,midg,midg; igrid,midg,midg -5.9714282E-08 1.3722811E-07 gauss-seidel spectral radius is 0.9888678 estimated iterations to convergence 77 setup time was (sec) 0.4000000 now iterating at: 08:15:38 rms-change max change #iterations 0.2036703 33.14227 at 10iterations 2.4189711E-02 3.555798 at 20iterations 3.8703417E-03 0.6647339 at 30iterations 1.1875173E-03 0.2374649 at 40iterations 4.7305832E-04 9.5947266E-02 at 50iterations finished qdiffx linear iterations at : 08:15:41 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.7305832E-04 9.5947266E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:15:42 3.426u 0.196s 0:03.93 91.8% 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 Tue Oct 11 2011 at 08:15:42 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.046212 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 2.046212 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 425.2113 centred at (gu) : 92.94345 90.00598 88.05370 assigned negative charge : -420.2124 centred at (gu) : 92.19194 89.91226 87.93496 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 92756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22946 grid for indexing accessible points = 1.400000 m= 35817 mr = 65901 m= 6482 mr = 27357 m= 505 mr = 4365 m= 7 mr = 246 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 0.4400000 number of dielectric boundary points 37698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20820 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) : 0.6820708 object centre at (A) : 30.21300 19.28300 -6.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1881664E-02 -2.2111541E-02 midg,1,midg; midg,igrid,midg 3.3664867E-02 2.6877958E-02 1,midg,midg; igrid,midg,midg -2.0344829E-02 9.1337517E-02 gauss-seidel spectral radius is 0.9988232 estimated iterations to convergence 231 setup time was (sec) 0.6500000 now iterating at: 08:15:43 rms-change max change #iterations 5.118521 259.8560 at 10iterations 2.521009 80.14759 at 20iterations 1.244085 36.78906 at 30iterations 0.6149840 21.44905 at 40iterations 0.3055611 8.066654 at 50iterations 0.1508204 4.086760 at 60iterations 7.4931502E-02 2.070105 at 70iterations 3.7374053E-02 1.095423 at 80iterations 1.8803440E-02 0.5207672 at 90iterations 9.6331425E-03 0.3075070 at 100iterations 5.1380545E-03 0.1676254 at 110iterations 2.8882436E-03 0.1005936 at 120iterations finished qdiffx linear iterations at : 08:15:50 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.8882436E-03 0.1005936 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:15:50 7.870u 0.228s 0:08.49 95.2% 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 Tue Oct 11 2011 at 08:15:50 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.069319 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): 4.116000 56.31000 ymin,ymax (A): -3.785000 42.35100 zmin,zma (A): -29.84800 17.34500 x,y,z range (A): 52.19400 46.13600 47.19300 scale (grids/A): 3.069319 object centre (A): 30.21300 19.28300 -6.251500 number of atom coordinates read : 2760 total number of charged atoms : 2625 net assigned charge : 5.000019 assigned positive charge : 425.2113 centred at (gu) : 94.41496 90.00880 87.08023 assigned negative charge : -420.2124 centred at (gu) : 93.28765 89.86825 86.90233 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 214206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22946 grid for indexing accessible points = 1.400000 m= 113129 mr = 159111 m= 44807 mr = 94211 m= 12083 mr = 37227 m= 2151 mr = 9367 m= 211 mr = 1598 m= 6 mr = 113 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 3519 time to turn everything in is 1.190000 number of dielectric boundary points 84967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 21000 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) : 2.046212 object centre at (A) : 30.21300 19.28300 -6.251500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3778452 -0.2739229 midg,1,midg; midg,igrid,midg 0.4017647 0.1756675 1,midg,midg; igrid,midg,midg -0.2932928 0.5239103 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 1.420000 now iterating at: 08:15:52 rms-change max change #iterations 11.55490 412.6326 at 10iterations 6.821873 123.1458 at 20iterations 4.026908 71.15558 at 30iterations 2.373104 42.71942 at 40iterations 1.393620 23.40347 at 50iterations 0.8207171 13.14242 at 60iterations 0.4821395 8.002033 at 70iterations 0.2834043 4.923260 at 80iterations 0.1660508 2.798706 at 90iterations 9.7433425E-02 1.760464 at 100iterations 5.7229288E-02 0.9568901 at 110iterations 3.3799943E-02 0.5328808 at 120iterations 2.0061268E-02 0.3716164 at 130iterations 1.2069364E-02 0.2037964 at 140iterations 7.4535236E-03 0.1406670 at 150iterations 4.8160413E-03 0.1008663 at 160iterations 3.3191550E-03 7.6164246E-02 at 170iterations 2.4413941E-03 5.8959961E-02 at 180iterations finished qdiffx linear iterations at : 08:16:03 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 2.4413941E-03 5.8959961E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 08:16:04 13.123u 0.232s 0:13.63 97.9% 0+0k 0+0io 0pf+0w