Wed Dec 28 11:02:52 PST 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 Wed Dec 28 2011 at 11:02:53 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6546404 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 0.6546404 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.2019 centred at (gu) : 90.27663 92.67600 90.02078 assigned negative charge : -288.8403 centred at (gu) : 90.39852 92.82527 89.94750 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5716 nv = 96 ne = 84 npr = 40563 no. pairs analyzed = 40563 no. exposed pairs = 2465 no. arc points = 17125 no. surface atoms = 832 nbur = 1134 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3190 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.2900000 number of dielectric boundary points 2812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1716 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6703 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4021275E-09 1.7287018E-08 midg,1,midg; midg,igrid,midg 1.5306384E-08 -2.0664196E-08 1,midg,midg; igrid,midg,midg 2.1951069E-08 -8.2149985E-09 gauss-seidel spectral radius is 0.9878492 estimated iterations to convergence 74 setup time was (sec) 0.7400000 now iterating at: 11:02:54 rms-change max change #iterations 0.1381270 18.47769 at 10iterations 1.4174617E-02 2.047911 at 20iterations 1.4907621E-03 0.2569389 at 30iterations 1.5128043E-04 2.1797180E-02 at 40iterations 1.5768952E-05 2.4595261E-03 at 50iterations finished qdiffx linear iterations at : 11:03:01 total time elapsed so far: 8.040000 # loops : 50 mean,max change (kT/e) : 1.5768952E-05 2.4595261E-03 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 11:03:02 8.205u 0.758s 0:09.48 94.4% 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 Wed Dec 28 2011 at 11:03:02 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.963921 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 1.963921 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.2019 centred at (gu) : 90.82966 98.02816 90.06248 assigned negative charge : -288.8403 centred at (gu) : 91.19589 98.47604 89.84268 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61628 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17125 grid for indexing accessible points = 1.400000 m= 23067 mr = 42759 m= 3729 mr = 17623 m= 227 mr = 2546 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1756 time to turn everything in is 0.5500000 number of dielectric boundary points 25642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 14475 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) : 0.6546404 object centre at (A) : 15.05200 22.32450 3.615500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0020833E-02 1.5109155E-02 midg,1,midg; midg,igrid,midg 4.8168000E-02 -9.2640631E-03 1,midg,midg; igrid,midg,midg 1.0275821E-02 -6.1987056E-03 gauss-seidel spectral radius is 0.9986346 estimated iterations to convergence 214 setup time was (sec) 0.8600000 now iterating at: 11:03:04 rms-change max change #iterations 3.832013 181.3485 at 10iterations 1.800245 68.06106 at 20iterations 0.8456650 29.93540 at 30iterations 0.3934337 12.97541 at 40iterations 0.1852345 6.295228 at 50iterations 8.6075135E-02 3.162156 at 60iterations 4.0361781E-02 1.383089 at 70iterations 1.8944716E-02 0.6359253 at 80iterations 8.8570798E-03 0.2811685 at 90iterations 4.1380166E-03 0.1393738 at 100iterations 1.9418030E-03 6.7671299E-02 at 110iterations 9.0935739E-04 3.4454346E-02 at 120iterations finished qdiffx linear iterations at : 11:03:20 total time elapsed so far: 17.66000 # loops : 120 mean,max change (kT/e) : 9.0935739E-04 3.4454346E-02 energy calculations done at 17.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 11:03:21 17.853u 0.738s 0:19.05 97.5% 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 Dec 28 2011 at 11:03:21 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.945882 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): -4.535000 34.63900 ymin,ymax (A): -3.577000 48.22600 zmin,zma (A): -23.57500 30.80600 x,y,z range (A): 39.17400 51.80300 54.38100 scale (grids/A): 2.945882 object centre (A): 15.05200 22.32450 3.615500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.2019 centred at (gu) : 91.24450 102.0422 90.09364 assigned negative charge : -288.8403 centred at (gu) : 91.79380 102.7142 89.76410 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 142341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17125 grid for indexing accessible points = 1.400000 m= 73531 mr = 103115 m= 27982 mr = 61362 m= 6936 mr = 23307 m= 1081 mr = 5493 m= 54 mr = 784 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5911 time to turn everything in is 1.600000 number of dielectric boundary points 57845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 14656 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) : 1.963921 object centre at (A) : 15.05200 22.32450 3.615500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.137874 4.0328633E-02 midg,1,midg; midg,igrid,midg 0.5023383 -0.1559473 1,midg,midg; igrid,midg,midg 6.9238849E-02 -3.5158385E-02 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 2.220000 now iterating at: 11:03:24 rms-change max change #iterations 8.918855 359.7021 at 10iterations 5.112492 120.4169 at 20iterations 2.919463 64.10143 at 30iterations 1.664699 36.53325 at 40iterations 0.9509875 17.99337 at 50iterations 0.5415905 10.99443 at 60iterations 0.3089175 6.339525 at 70iterations 0.1762092 3.527033 at 80iterations 0.1003355 1.937584 at 90iterations 5.7302881E-02 1.042495 at 100iterations 3.2634519E-02 0.6474533 at 110iterations 1.8591369E-02 0.4081616 at 120iterations 1.0607916E-02 0.2122898 at 130iterations 6.0529239E-03 0.1215897 at 140iterations 3.4469445E-03 6.6311836E-02 at 150iterations 1.9645845E-03 3.8379192E-02 at 160iterations 1.1214295E-03 2.1315575E-02 at 170iterations 6.4078468E-04 1.2204170E-02 at 180iterations finished qdiffx linear iterations at : 11:03:52 total time elapsed so far: 29.76000 # loops : 180 mean,max change (kT/e) : 6.4078468E-04 1.2204170E-02 energy calculations done at 29.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.93000 DelPhi exited at 11:03:53 29.937u 0.945s 0:31.42 98.2% 0+0k 0+0io 0pf+0w