Mon Oct 10 19:35:41 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 Mon Oct 10 2011 at 19:35:41 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6055245 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 0.6055245 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.485967 assigned positive charge : 394.7007 centred at (gu) : 90.58504 89.69452 90.75816 assigned negative charge : -398.1874 centred at (gu) : 90.66435 89.89516 90.81940 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6325 nv = 96 ne = 84 npr = 53394 no. pairs analyzed = 53394 no. exposed pairs = 3503 no. arc points = 24728 no. surface atoms = 1171 nbur = 1453 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3172 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2100000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2437 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7735685E-10 -5.3287192E-09 midg,1,midg; midg,igrid,midg 7.4482278E-09 -1.0130617E-08 1,midg,midg; igrid,midg,midg 1.5015849E-09 -6.0555521E-09 gauss-seidel spectral radius is 0.9858872 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 19:35:41 rms-change max change #iterations 0.1126030 19.09269 at 10iterations 9.6233003E-03 1.438263 at 20iterations 8.4585033E-04 0.1439400 at 30iterations 7.4019721E-05 1.1627197E-02 at 40iterations 6.6477569E-06 1.1596680E-03 at 50iterations finished qdiffx linear iterations at : 19:35:44 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.6477569E-06 1.1596680E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:35:45 3.417u 0.160s 0:03.96 90.1% 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 Mon Oct 10 2011 at 19:35:45 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.816574 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 1.816574 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.485967 assigned positive charge : 394.7007 centred at (gu) : 91.75445 89.08320 92.27380 assigned negative charge : -398.1874 centred at (gu) : 91.99277 89.68509 92.45793 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24728 grid for indexing accessible points = 1.400000 m= 22463 mr = 45234 m= 3114 mr = 15461 m= 167 mr = 1617 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1034 time to turn everything in is 0.3500000 number of dielectric boundary points 31657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19413 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) : 0.6055245 object centre at (A) : -0.6359997 35.77250 22.21750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6867044E-03 -9.9007795E-03 midg,1,midg; midg,igrid,midg 1.8378846E-02 -2.8111385E-02 1,midg,midg; igrid,midg,midg -2.8218383E-03 -5.3271079E-03 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 0.5600000 now iterating at: 19:35:45 rms-change max change #iterations 3.925267 172.1489 at 10iterations 1.766946 68.08217 at 20iterations 0.7927662 28.73682 at 30iterations 0.3589833 12.62592 at 40iterations 0.1616998 5.605330 at 50iterations 7.3054396E-02 2.570339 at 60iterations 3.2947838E-02 1.116894 at 70iterations 1.4894910E-02 0.5411415 at 80iterations 6.7287306E-03 0.2406540 at 90iterations 3.0352483E-03 0.1044235 at 100iterations 1.3699295E-03 4.3666840E-02 at 110iterations 6.1821030E-04 2.2188187E-02 at 120iterations finished qdiffx linear iterations at : 19:35:52 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 6.1821030E-04 2.2188187E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 19:35:53 7.749u 0.215s 0:08.39 94.7% 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 Mon Oct 10 2011 at 19:35:53 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2624 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.724860 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): -30.03200 28.76000 ymin,ymax (A): 12.54400 59.00100 zmin,zma (A): -1.855000 46.29000 x,y,z range (A): 58.79200 46.45700 48.14500 scale (grids/A): 2.724860 object centre (A): -0.6359997 35.77250 22.21750 number of atom coordinates read : 2624 total number of charged atoms : 2485 net assigned charge : -3.485967 assigned positive charge : 394.7007 centred at (gu) : 92.63142 88.62469 93.41049 assigned negative charge : -398.1874 centred at (gu) : 92.98900 89.52764 93.68679 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 158338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24728 grid for indexing accessible points = 1.400000 m= 74264 mr = 111163 m= 24597 mr = 58195 m= 5167 mr = 18520 m= 606 mr = 3385 m= 36 mr = 304 m= 0 mr = 3 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 3468 time to turn everything in is 0.8700000 number of dielectric boundary points 71438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19878 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) : 1.816574 object centre at (A) : -0.6359997 35.77250 22.21750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3945651E-02 -8.4743358E-02 midg,1,midg; midg,igrid,midg 0.2510373 -0.2786258 1,midg,midg; igrid,midg,midg 0.1834740 0.1323610 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.100000 now iterating at: 19:35:54 rms-change max change #iterations 9.627401 290.8931 at 10iterations 5.633672 151.2589 at 20iterations 3.261325 97.66046 at 30iterations 1.882962 46.68169 at 40iterations 1.081675 25.12646 at 50iterations 0.6207755 13.77948 at 60iterations 0.3550427 7.665997 at 70iterations 0.2029376 4.690564 at 80iterations 0.1158398 2.264162 at 90iterations 6.6123001E-02 1.289989 at 100iterations 3.7628636E-02 0.7749939 at 110iterations 2.1456188E-02 0.4403076 at 120iterations 1.2213655E-02 0.2471080 at 130iterations 6.9537438E-03 0.1291275 at 140iterations 3.9639524E-03 7.1627140E-02 at 150iterations 2.2544009E-03 4.2594910E-02 at 160iterations 1.2836116E-03 2.8041840E-02 at 170iterations 7.2966446E-04 1.5430689E-02 at 180iterations finished qdiffx linear iterations at : 19:36:06 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 7.2966446E-04 1.5430689E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 19:36:06 12.475u 0.207s 0:12.96 97.7% 0+0k 0+0io 0pf+0w