Sat Oct 8 22:35:22 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 Sat Oct 8 2011 at 22:35:22 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 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: 0.6657317 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 0.6657317 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 343.4683 centred at (gu) : 90.43060 90.98090 92.01984 assigned negative charge : -331.9690 centred at (gu) : 90.46554 90.94055 91.99998 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7242 nv = 96 ne = 84 npr = 46336 no. pairs analyzed = 46336 no. exposed pairs = 3161 no. arc points = 22525 no. surface atoms = 1055 nbur = 1283 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3810 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2700000 number of dielectric boundary points 3832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2220 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0161945E-08 5.6650403E-08 midg,1,midg; midg,igrid,midg 2.1394394E-08 5.0721599E-08 1,midg,midg; igrid,midg,midg 3.7199143E-08 2.9318100E-08 gauss-seidel spectral radius is 0.9882911 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 22:35:23 rms-change max change #iterations 0.1568106 28.29609 at 10iterations 1.6994363E-02 2.368398 at 20iterations 1.9580135E-03 0.2330770 at 30iterations 3.6974982E-04 5.9600830E-02 at 40iterations 1.3157593E-04 2.0069122E-02 at 50iterations finished qdiffx linear iterations at : 22:35:26 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.3157593E-04 2.0069122E-02 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 22:35:27 4.131u 0.241s 0:04.64 94.1% 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 Sat Oct 8 2011 at 22:35:27 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 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: 1.997195 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 1.997195 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 343.4683 centred at (gu) : 91.29149 92.94229 96.05927 assigned negative charge : -331.9690 centred at (gu) : 91.39672 92.82172 95.99987 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22525 grid for indexing accessible points = 1.400000 m= 28512 mr = 51125 m= 5271 mr = 20683 m= 460 mr = 3318 m= 5 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1769 time to turn everything in is 0.5800000 number of dielectric boundary points 35194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17414 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) : 0.6657317 object centre at (A) : -0.4045000 28.87250 13.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3619037E-02 4.0730614E-02 midg,1,midg; midg,igrid,midg 5.5499333E-03 3.2481343E-02 1,midg,midg; igrid,midg,midg 6.3105106E-02 6.3443072E-02 gauss-seidel spectral radius is 0.9987385 estimated iterations to convergence 223 setup time was (sec) 0.9100000 now iterating at: 22:35:28 rms-change max change #iterations 4.321465 233.0555 at 10iterations 2.089202 77.29595 at 20iterations 1.003209 36.78893 at 30iterations 0.4829289 14.26267 at 40iterations 0.2330314 7.516035 at 50iterations 0.1123489 3.363307 at 60iterations 5.4217417E-02 1.704243 at 70iterations 2.6202315E-02 0.8250265 at 80iterations 1.2628188E-02 0.4298711 at 90iterations 6.1062807E-03 0.2020111 at 100iterations 3.0044168E-03 8.8016510E-02 at 110iterations 1.4985036E-03 4.6045303E-02 at 120iterations finished qdiffx linear iterations at : 22:35:37 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.4985036E-03 4.6045303E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 22:35:37 9.621u 0.247s 0:10.16 97.0% 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 Sat Oct 8 2011 at 22:35:37 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2338 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: 2.995793 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): -27.14200 26.33300 ymin,ymax (A): 8.037000 49.70800 zmin,zma (A): -12.95900 39.46400 x,y,z range (A): 53.47500 41.67100 52.42300 scale (grids/A): 2.995793 object centre (A): -0.4045000 28.87250 13.25250 number of atom coordinates read : 2338 total number of charged atoms : 2203 net assigned charge : 11.50002 assigned positive charge : 343.4683 centred at (gu) : 91.93724 94.41328 99.08880 assigned negative charge : -331.9690 centred at (gu) : 92.09505 94.23255 98.99979 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22525 grid for indexing accessible points = 1.400000 m= 89626 mr = 124389 m= 35056 mr = 72310 m= 9773 mr = 27895 m= 1816 mr = 7360 m= 178 mr = 1280 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 5918 time to turn everything in is 1.550000 number of dielectric boundary points 79362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 17624 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) : 1.997195 object centre at (A) : -0.4045000 28.87250 13.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5383858 0.3979229 midg,1,midg; midg,igrid,midg 2.4396133E-02 0.3147566 1,midg,midg; igrid,midg,midg 0.6375960 0.5670123 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.890000 now iterating at: 22:35:39 rms-change max change #iterations 10.14162 438.6067 at 10iterations 6.062269 135.4331 at 20iterations 3.618523 75.25533 at 30iterations 2.148772 42.24555 at 40iterations 1.269788 25.24472 at 50iterations 0.7494200 15.59672 at 60iterations 0.4405587 9.778052 at 70iterations 0.2587211 4.878856 at 80iterations 0.1516627 2.768226 at 90iterations 8.8874206E-02 1.707572 at 100iterations 5.2077498E-02 0.9429226 at 110iterations 3.0412005E-02 0.6636677 at 120iterations 1.7852075E-02 0.3023983 at 130iterations 1.0422132E-02 0.1898143 at 140iterations 6.1280639E-03 0.1062403 at 150iterations 3.6354775E-03 7.2635651E-02 at 160iterations 2.1776478E-03 5.2347183E-02 at 170iterations 1.3402526E-03 2.6493073E-02 at 180iterations finished qdiffx linear iterations at : 22:35:53 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 1.3402526E-03 2.6493073E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 22:35:53 15.559u 0.277s 0:16.10 98.2% 0+0k 0+0io 0pf+0w