Wed Feb 15 08:56:24 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:24 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 = 2698 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: 0.5954871 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 0.5954871 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.10321 88.94218 90.14370 assigned negative charge : -386.9133 centred at (gu) : 90.05016 88.91851 90.25134 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6435 nv = 96 ne = 84 npr = 54167 no. pairs analyzed = 54167 no. exposed pairs = 3571 no. arc points = 25218 no. surface atoms = 1196 nbur = 1502 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 = 1.456000 m= 295 mr = 3280 m= 0 mr = 16 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 3434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2545 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4791301E-09 -1.1364248E-10 midg,1,midg; midg,igrid,midg 3.2628324E-09 3.2284886E-09 1,midg,midg; igrid,midg,midg 1.6164363E-09 5.1198543E-09 gauss-seidel spectral radius is 0.9854224 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 08:56:25 rms-change max change #iterations 0.1057101 17.78112 at 10iterations 8.7989774E-03 1.473084 at 20iterations 7.1287068E-04 0.1059265 at 30iterations 6.1144339E-05 1.0194302E-02 at 40iterations 5.2205610E-06 1.2168884E-03 at 50iterations finished qdiffx linear iterations at : 08:56:28 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.2205610E-06 1.2168884E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 08:56:28 3.477u 0.163s 0:04.03 90.0% 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 Wed Feb 15 2012 at 08:56:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 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: 1.786461 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 1.786461 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.30917 86.82564 90.43031 assigned negative charge : -386.9133 centred at (gu) : 90.15019 86.75510 90.75380 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 69988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25218 grid for indexing accessible points = 1.400000 m= 23038 mr = 46774 m= 3054 mr = 16006 m= 134 mr = 1550 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 104 time to turn everything in is 0.6200000 number of dielectric boundary points 31852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19986 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) : 0.5954871 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0338055E-02 1.2372162E-02 midg,1,midg; midg,igrid,midg 1.6986294E-02 4.9311569E-04 1,midg,midg; igrid,midg,midg 5.7197949E-03 7.6686451E-03 gauss-seidel spectral radius is 0.9984682 estimated iterations to convergence 203 setup time was (sec) 0.9200000 now iterating at: 08:56:29 rms-change max change #iterations 3.688299 177.6100 at 10iterations 1.641227 63.85879 at 20iterations 0.7331330 24.61906 at 30iterations 0.3280369 11.68579 at 40iterations 0.1463153 5.081567 at 50iterations 6.5262131E-02 2.182431 at 60iterations 2.9138949E-02 0.9978313 at 70iterations 1.3009336E-02 0.4220715 at 80iterations 5.8280523E-03 0.1955414 at 90iterations 2.6136462E-03 9.4703674E-02 at 100iterations 1.1707869E-03 3.8370132E-02 at 110iterations 5.2321318E-04 1.8534660E-02 at 120iterations finished qdiffx linear iterations at : 08:56:36 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 5.2321318E-04 1.8534660E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 08:56:36 7.717u 0.211s 0:08.23 96.2% 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 Wed Feb 15 2012 at 08:56:36 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 = 2698 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: 2.679692 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): -21.64300 29.45000 ymin,ymax (A): -26.83800 32.94500 zmin,zma (A): -6.174000 50.98200 x,y,z range (A): 51.09300 59.78300 57.15600 scale (grids/A): 2.679692 object centre (A): 3.903500 3.053500 22.40400 number of atom coordinates read : 2698 total number of charged atoms : 2561 net assigned charge : 9.000017 assigned positive charge : 395.9126 centred at (gu) : 90.46369 85.23846 90.64529 assigned negative charge : -386.9133 centred at (gu) : 90.22519 85.13254 91.13065 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25218 grid for indexing accessible points = 1.400000 m= 76447 mr = 114191 m= 24959 mr = 60522 m= 5111 mr = 18834 m= 558 mr = 3421 m= 27 mr = 301 m= 0 mr = 8 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 1.400000 number of dielectric boundary points 71905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 20485 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) : 1.786461 object centre at (A) : 3.903500 3.053500 22.40400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6080718 0.1589920 midg,1,midg; midg,igrid,midg 0.3176250 4.2236507E-02 1,midg,midg; igrid,midg,midg 8.6121343E-02 6.1686445E-02 gauss-seidel spectral radius is 0.9992216 estimated iterations to convergence 283 setup time was (sec) 1.740000 now iterating at: 08:56:38 rms-change max change #iterations 9.079802 410.7865 at 10iterations 5.250548 137.3749 at 20iterations 3.011307 78.56170 at 30iterations 1.722859 45.60707 at 40iterations 0.9799168 24.44268 at 50iterations 0.5576531 13.13655 at 60iterations 0.3170499 6.548467 at 70iterations 0.1800949 3.837017 at 80iterations 0.1018333 1.978088 at 90iterations 5.7656690E-02 1.181917 at 100iterations 3.2789309E-02 0.6958194 at 110iterations 1.8605877E-02 0.3760376 at 120iterations 1.0490573E-02 0.2017493 at 130iterations 5.9389020E-03 0.1151552 at 140iterations 3.3765668E-03 6.6467285E-02 at 150iterations 1.9090479E-03 3.5657406E-02 at 160iterations 1.0814106E-03 1.9855976E-02 at 170iterations 6.1319070E-04 1.1432648E-02 at 180iterations finished qdiffx linear iterations at : 08:56:53 total time elapsed so far: 16.11000 # loops : 180 mean,max change (kT/e) : 6.1319070E-04 1.1432648E-02 energy calculations done at 16.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 08:56:53 16.330u 0.232s 0:16.96 97.6% 0+0k 0+0io 0pf+0w