Sun Oct 9 11:58:18 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 11:58:18 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: HIQ 202 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6650973 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 0.6650973 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5140090 assigned positive charge : 385.7263 centred at (gu) : 89.32018 89.56870 92.65864 assigned negative charge : -385.2138 centred at (gu) : 89.48892 89.65411 92.57271 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8548 nv = 96 ne = 84 npr = 52942 no. pairs analyzed = 52942 no. exposed pairs = 3638 no. arc points = 26182 no. surface atoms = 1232 nbur = 1448 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 592 mr = 4510 m= 0 mr = 112 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0712492E-08 3.4366501E-08 midg,1,midg; midg,igrid,midg 2.1207113E-08 -1.6916442E-08 1,midg,midg; igrid,midg,midg 4.3137938E-08 -3.2517580E-08 gauss-seidel spectral radius is 0.9883112 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 11:58:19 rms-change max change #iterations 0.1744931 25.03181 at 10iterations 1.9082421E-02 2.487839 at 20iterations 2.2139286E-03 0.2983665 at 30iterations 3.8874467E-04 6.5065384E-02 at 40iterations 1.1186325E-04 2.1188736E-02 at 50iterations finished qdiffx linear iterations at : 11:58:22 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1186325E-04 2.1188736E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:58:22 3.413u 0.141s 0:03.85 92.2% 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 Sun Oct 9 2011 at 11:58:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: HIQ 202 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.995292 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 1.995292 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5140090 assigned positive charge : 385.7263 centred at (gu) : 87.95969 88.70525 97.97523 assigned negative charge : -385.2138 centred at (gu) : 88.46676 88.96194 97.71802 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26182 grid for indexing accessible points = 1.400000 m= 34899 mr = 60508 m= 7398 mr = 25353 m= 628 mr = 4956 m= 4 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.6800000 number of dielectric boundary points 41737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20106 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) : 0.6650973 object centre at (A) : 77.64700 31.05300 61.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3892811E-02 7.8890823E-02 midg,1,midg; midg,igrid,midg 2.2757564E-02 -1.2145230E-02 1,midg,midg; igrid,midg,midg 2.9088518E-02 -4.4512700E-02 gauss-seidel spectral radius is 0.9987891 estimated iterations to convergence 228 setup time was (sec) 0.9700000 now iterating at: 11:58:23 rms-change max change #iterations 4.698567 192.5793 at 10iterations 2.308831 81.87998 at 20iterations 1.130183 32.20235 at 30iterations 0.5535475 16.99192 at 40iterations 0.2717259 7.726471 at 50iterations 0.1332196 3.926014 at 60iterations 6.5301701E-02 1.783154 at 70iterations 3.2016587E-02 0.9530574 at 80iterations 1.5706416E-02 0.4344347 at 90iterations 7.7022458E-03 0.2184067 at 100iterations 3.8059896E-03 0.1262093 at 110iterations 1.8882763E-03 5.1738739E-02 at 120iterations finished qdiffx linear iterations at : 11:58:30 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.8882763E-03 5.1738739E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 11:58:31 7.805u 0.168s 0:08.25 96.4% 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 Sun Oct 9 2011 at 11:58:31 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: HIQ 202 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.992938 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 2.992938 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5140090 assigned positive charge : 385.7263 centred at (gu) : 86.93929 88.05763 101.9626 assigned negative charge : -385.2138 centred at (gu) : 87.70018 88.44276 101.5770 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 207266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26182 grid for indexing accessible points = 1.400000 m= 107242 mr = 146852 m= 45363 mr = 86494 m= 13958 mr = 36401 m= 2846 mr = 10789 m= 234 mr = 2126 m= 5 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 1.730000 number of dielectric boundary points 94119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 20312 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) : 1.995292 object centre at (A) : 77.64700 31.05300 61.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1264402 0.9960276 midg,1,midg; midg,igrid,midg 0.2369779 -0.3307984 1,midg,midg; igrid,midg,midg 0.2157400 -0.4032529 gauss-seidel spectral radius is 0.9993250 estimated iterations to convergence 304 setup time was (sec) 2.050000 now iterating at: 11:58:33 rms-change max change #iterations 10.91979 488.0544 at 10iterations 6.624203 159.1231 at 20iterations 3.989431 92.62254 at 30iterations 2.397125 54.78954 at 40iterations 1.434397 29.01680 at 50iterations 0.8540694 16.19808 at 60iterations 0.5088400 9.580009 at 70iterations 0.3021449 5.243270 at 80iterations 0.1789894 3.268579 at 90iterations 0.1060939 1.797293 at 100iterations 6.2744565E-02 1.139801 at 110iterations 3.7140384E-02 0.6805248 at 120iterations 2.1974210E-02 0.3638983 at 130iterations 1.2965973E-02 0.2142563 at 140iterations 7.6876734E-03 0.1301403 at 150iterations 4.5657777E-03 7.6896667E-02 at 160iterations 2.7054867E-03 4.2922974E-02 at 170iterations 1.6250610E-03 2.7997971E-02 at 180iterations finished qdiffx linear iterations at : 11:58:43 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.6250610E-03 2.7997971E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 11:58:44 12.937u 0.191s 0:13.40 97.9% 0+0k 0+0io 0pf+0w