Sun Oct 9 21:28:26 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 Sun Oct 9 2011 at 21:28:26 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: ZN6 654 has a net charge of 1.4000 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: 0.6513585 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 0.6513585 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2427 net assigned charge : 7.025008 assigned positive charge : 390.7979 centred at (gu) : 90.81747 89.64040 90.10712 assigned negative charge : -383.7736 centred at (gu) : 90.80084 89.47011 90.09283 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7366 nv = 96 ne = 84 npr = 48878 no. pairs analyzed = 48878 no. exposed pairs = 3251 no. arc points = 23006 no. surface atoms = 1109 nbur = 1427 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3967 m= 0 mr = 64 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3000000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1702122E-08 1.6787119E-08 midg,1,midg; midg,igrid,midg -1.4019122E-08 3.7388489E-08 1,midg,midg; igrid,midg,midg 9.8446860E-09 1.9866860E-08 gauss-seidel spectral radius is 0.9877872 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 21:28:26 rms-change max change #iterations 0.1554755 20.89376 at 10iterations 1.6028475E-02 2.339801 at 20iterations 1.6572539E-03 0.2229843 at 30iterations 1.7461950E-04 2.8987885E-02 at 40iterations 1.8009527E-05 2.7208328E-03 at 50iterations finished qdiffx linear iterations at : 21:28:29 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.8009527E-05 2.7208328E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 21:28:30 3.676u 0.222s 0:04.19 92.8% 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 Sun Oct 9 2011 at 21:28:30 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: ZN6 654 has a net charge of 1.4000 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: 1.954076 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 1.954076 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2427 net assigned charge : 7.025008 assigned positive charge : 390.7979 centred at (gu) : 92.45171 88.92067 90.32112 assigned negative charge : -383.7736 centred at (gu) : 92.40241 88.41021 90.27831 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23006 grid for indexing accessible points = 1.400000 m= 29609 mr = 54377 m= 5228 mr = 21787 m= 399 mr = 3356 m= 8 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 0.6000000 number of dielectric boundary points 34980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19147 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) : 0.6513585 object centre at (A) : 13.14550 5.134501 14.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3204218E-02 -1.1007784E-02 midg,1,midg; midg,igrid,midg 1.4454072E-02 5.5467382E-02 1,midg,midg; igrid,midg,midg -6.8053952E-03 1.6087471E-02 gauss-seidel spectral radius is 0.9986993 estimated iterations to convergence 220 setup time was (sec) 0.9300000 now iterating at: 21:28:31 rms-change max change #iterations 4.418977 179.4171 at 10iterations 2.095572 72.29339 at 20iterations 0.9977525 31.26178 at 30iterations 0.4758509 16.36784 at 40iterations 0.2260032 6.889345 at 50iterations 0.1077318 3.203368 at 60iterations 5.1303450E-02 1.822918 at 70iterations 2.4431441E-02 0.8763123 at 80iterations 1.1639955E-02 0.3556366 at 90iterations 5.5413139E-03 0.1789093 at 100iterations 2.6407284E-03 8.5133553E-02 at 110iterations 1.2615457E-03 4.3769836E-02 at 120iterations finished qdiffx linear iterations at : 21:28:38 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.2615457E-03 4.3769836E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 21:28:39 8.449u 0.248s 0:08.96 96.8% 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 Sun Oct 9 2011 at 21:28:39 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: ZN6 654 has a net charge of 1.4000 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: 2.931113 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 2.931113 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2427 net assigned charge : 7.025008 assigned positive charge : 390.7979 centred at (gu) : 93.67751 88.38106 90.48149 assigned negative charge : -383.7736 centred at (gu) : 93.60355 87.61520 90.41739 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 183326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23006 grid for indexing accessible points = 1.400000 m= 93977 mr = 131586 m= 35889 mr = 76847 m= 9533 mr = 28776 m= 1703 mr = 7280 m= 163 mr = 1189 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1489 time to turn everything in is 1.570000 number of dielectric boundary points 78813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 19416 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) : 1.954076 object centre at (A) : 13.14550 5.134501 14.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2595750 -0.2996472 midg,1,midg; midg,igrid,midg 2.8066641E-02 0.6002888 1,midg,midg; igrid,midg,midg -0.2127271 0.2403123 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 1.920000 now iterating at: 21:28:41 rms-change max change #iterations 10.29230 389.1010 at 10iterations 6.027918 139.6446 at 20iterations 3.521369 72.86633 at 30iterations 2.049689 42.14391 at 40iterations 1.193423 20.89985 at 50iterations 0.6941643 12.08786 at 60iterations 0.4021112 7.871252 at 70iterations 0.2334415 3.899200 at 80iterations 0.1350916 2.411297 at 90iterations 7.8424573E-02 1.334166 at 100iterations 4.5313627E-02 0.7660261 at 110iterations 2.6262404E-02 0.4847717 at 120iterations 1.5217506E-02 0.2548800 at 130iterations 8.8239796E-03 0.1473341 at 140iterations 5.0892518E-03 8.8397503E-02 at 150iterations 2.9578193E-03 5.1219940E-02 at 160iterations 1.7098360E-03 3.0517578E-02 at 170iterations 9.8883605E-04 1.7248631E-02 at 180iterations finished qdiffx linear iterations at : 21:28:54 total time elapsed so far: 15.29000 # loops : 180 mean,max change (kT/e) : 9.8883605E-04 1.7248631E-02 energy calculations done at 15.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 21:28:55 15.478u 0.289s 0:16.03 98.2% 0+0k 0+0io 0pf+0w