Sun Oct 9 17:20:44 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 Sun Oct 9 2011 at 17:20:44 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5042 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5640140 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): 3.227000 64.99000 ymin,ymax (A): -8.570000 53.47300 zmin,zma (A): -1.162000 61.95700 x,y,z range (A): 61.76300 62.04300 63.11900 scale (grids/A): 0.5640140 object centre (A): 34.10850 22.45150 30.39750 number of atom coordinates read : 5042 total number of charged atoms : 4896 net assigned charge : -0.8789544 assigned positive charge : 773.8338 centred at (gu) : 88.32272 89.24617 89.16766 assigned negative charge : -774.7186 centred at (gu) : 88.20180 89.27072 89.13798 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10533 nv = 96 ne = 84 npr = 101949 no. pairs analyzed = 101949 no. exposed pairs = 6000 no. arc points = 40327 no. surface atoms = 2042 nbur = 3000 mkacc time = 0.1700000 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 = 1.540000 m= 507 mr = 6060 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4114 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13772 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7476254E-10 4.8906224E-10 midg,1,midg; midg,igrid,midg 5.8734850E-10 -5.0001220E-10 1,midg,midg; igrid,midg,midg -4.1924224E-09 1.7201088E-09 gauss-seidel spectral radius is 0.9839370 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 17:20:44 rms-change max change #iterations 0.1177450 15.19864 at 10iterations 1.0761209E-02 1.370224 at 20iterations 2.9259704E-03 0.3249359 at 30iterations 1.3538821E-03 0.1432648 at 40iterations 6.5759599E-04 7.5503588E-02 at 50iterations finished qdiffx linear iterations at : 17:20:47 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.5759599E-04 7.5503588E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 17:20:48 3.587u 0.195s 0:04.06 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 17:20:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5042 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.692042 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): 3.227000 64.99000 ymin,ymax (A): -8.570000 53.47300 zmin,zma (A): -1.162000 61.95700 x,y,z range (A): 61.76300 62.04300 63.11900 scale (grids/A): 1.692042 object centre (A): 34.10850 22.45150 30.39750 number of atom coordinates read : 5042 total number of charged atoms : 4896 net assigned charge : -0.8789544 assigned positive charge : 773.8338 centred at (gu) : 84.96663 87.73714 87.50154 assigned negative charge : -774.7186 centred at (gu) : 84.60517 87.81245 87.41383 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 117194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40327 grid for indexing accessible points = 1.400000 m= 41721 mr = 84909 m= 5309 mr = 30254 m= 178 mr = 2890 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 46326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 356 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 37748 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) : 0.5640140 object centre at (A) : 34.10850 22.45150 30.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0100500E-02 -2.8573098E-02 midg,1,midg; midg,igrid,midg 1.6599109E-02 9.8876432E-03 1,midg,midg; igrid,midg,midg -2.9862845E-02 2.6860356E-02 gauss-seidel spectral radius is 0.9985020 estimated iterations to convergence 205 setup time was (sec) 0.8000000 now iterating at: 17:20:49 rms-change max change #iterations 5.010528 192.2669 at 10iterations 2.255220 61.70527 at 20iterations 1.021530 30.78070 at 30iterations 0.4632059 12.12584 at 40iterations 0.2093887 6.019937 at 50iterations 9.5447026E-02 2.577402 at 60iterations 4.3630954E-02 1.227852 at 70iterations 2.0385133E-02 0.5529256 at 80iterations 9.9796392E-03 0.3267822 at 90iterations 5.4029063E-03 0.1540794 at 100iterations 3.3323595E-03 8.7532043E-02 at 110iterations 2.3289723E-03 5.5873871E-02 at 120iterations finished qdiffx linear iterations at : 17:20:56 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 2.3289723E-03 5.5873871E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 17:20:57 8.303u 0.194s 0:08.79 96.5% 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 Sun Oct 9 2011 at 17:20:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5042 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.538063 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): 3.227000 64.99000 ymin,ymax (A): -8.570000 53.47300 zmin,zma (A): -1.162000 61.95700 x,y,z range (A): 61.76300 62.04300 63.11900 scale (grids/A): 2.538063 object centre (A): 34.10850 22.45150 30.39750 number of atom coordinates read : 5042 total number of charged atoms : 4896 net assigned charge : -0.8789544 assigned positive charge : 773.8338 centred at (gu) : 82.44957 86.60548 86.25207 assigned negative charge : -774.7186 centred at (gu) : 81.90770 86.71864 86.12075 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 272166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40327 grid for indexing accessible points = 1.400000 m= 139100 mr = 206370 m= 45354 mr = 113472 m= 8859 mr = 35237 m= 811 mr = 6158 m= 21 mr = 425 m= 0 mr = 4 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 104645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 39142 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) : 1.692042 object centre at (A) : 34.10850 22.45150 30.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4787191 -0.6730763 midg,1,midg; midg,igrid,midg -2.0515060E-02 -4.1678031E-03 1,midg,midg; igrid,midg,midg -0.4695939 0.3134656 gauss-seidel spectral radius is 0.9992743 estimated iterations to convergence 293 setup time was (sec) 1.680000 now iterating at: 17:20:58 rms-change max change #iterations 12.61061 319.4935 at 10iterations 7.488016 156.8284 at 20iterations 4.424935 86.04586 at 30iterations 2.607730 48.81131 at 40iterations 1.529355 26.81505 at 50iterations 0.8942361 14.80030 at 60iterations 0.5213265 8.475908 at 70iterations 0.3039193 4.958893 at 80iterations 0.1767692 2.815555 at 90iterations 0.1029373 1.818859 at 100iterations 5.9708491E-02 0.9751325 at 110iterations 3.4924213E-02 0.5442276 at 120iterations 2.0456683E-02 0.3302174 at 130iterations 1.2172947E-02 0.1980209 at 140iterations 7.4205045E-03 0.1173506 at 150iterations 4.7119474E-03 7.5645447E-02 at 160iterations 3.1987543E-03 5.9585571E-02 at 170iterations 2.3419792E-03 3.5766602E-02 at 180iterations finished qdiffx linear iterations at : 17:21:10 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 2.3419792E-03 3.5766602E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 17:21:11 13.830u 0.226s 0:14.33 98.0% 0+0k 0+0io 0pf+0w