Mon Oct 10 18:45:10 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 Mon Oct 10 2011 at 18:45:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 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: 0.6937814 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 0.6937814 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000003 assigned positive charge : 341.6541 centred at (gu) : 89.22794 86.40606 88.38711 assigned negative charge : -339.6547 centred at (gu) : 89.20776 86.53653 88.34737 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7339 nv = 96 ne = 84 npr = 47989 no. pairs analyzed = 47989 no. exposed pairs = 2927 no. arc points = 20303 no. surface atoms = 980 nbur = 1322 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4001 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3100000 number of dielectric boundary points 3766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1870 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8453 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5556459E-09 1.8699026E-08 midg,1,midg; midg,igrid,midg 1.2594850E-07 -1.9822860E-08 1,midg,midg; igrid,midg,midg 2.7232592E-09 1.5573207E-08 gauss-seidel spectral radius is 0.9891981 estimated iterations to convergence 78 setup time was (sec) 0.5400000 now iterating at: 18:45:11 rms-change max change #iterations 0.1933896 25.44397 at 10iterations 2.2435699E-02 3.453327 at 20iterations 2.6443270E-03 0.3329611 at 30iterations 3.2636549E-04 4.0658951E-02 at 40iterations 4.1269584E-05 5.8860779E-03 at 50iterations finished qdiffx linear iterations at : 18:45:13 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 4.1269584E-05 5.8860779E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 18:45:14 3.321u 0.144s 0:03.75 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 Mon Oct 10 2011 at 18:45:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 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: 2.081344 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 2.081344 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000003 assigned positive charge : 341.6541 centred at (gu) : 87.68321 79.21796 85.16087 assigned negative charge : -339.6547 centred at (gu) : 87.62315 79.60954 85.04184 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20303 grid for indexing accessible points = 1.400000 m= 30198 mr = 52837 m= 6207 mr = 22539 m= 545 mr = 4102 m= 18 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1341 time to turn everything in is 0.6000000 number of dielectric boundary points 34441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17208 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) : 0.6937814 object centre at (A) : 50.69400 43.05450 30.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1699788E-02 4.0732920E-02 midg,1,midg; midg,igrid,midg 3.0700918E-02 -2.6556624E-02 1,midg,midg; igrid,midg,midg 1.7473526E-02 6.5771081E-03 gauss-seidel spectral radius is 0.9988112 estimated iterations to convergence 230 setup time was (sec) 0.8700000 now iterating at: 18:45:15 rms-change max change #iterations 4.661945 190.0347 at 10iterations 2.290102 79.71568 at 20iterations 1.126067 33.82035 at 30iterations 0.5572404 18.74391 at 40iterations 0.2746814 8.244770 at 50iterations 0.1349693 3.853769 at 60iterations 6.6619106E-02 1.965303 at 70iterations 3.2767911E-02 0.9633265 at 80iterations 1.6125668E-02 0.4508209 at 90iterations 7.9709748E-03 0.2477417 at 100iterations 3.9263768E-03 0.1140060 at 110iterations 1.9358362E-03 5.6464195E-02 at 120iterations finished qdiffx linear iterations at : 18:45:21 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 1.9358362E-03 5.6464195E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 18:45:22 7.443u 0.194s 0:08.31 91.8% 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 Mon Oct 10 2011 at 18:45:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 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: 3.122016 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 3.122016 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000003 assigned positive charge : 341.6541 centred at (gu) : 86.52463 73.82677 82.74124 assigned negative charge : -339.6547 centred at (gu) : 86.43472 74.41425 82.56273 start vw surface at 0.1800000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 177762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20303 grid for indexing accessible points = 1.400000 m= 92531 mr = 127670 m= 39194 mr = 75773 m= 11824 mr = 31996 m= 2294 mr = 9132 m= 276 mr = 1606 m= 14 mr = 162 m= 0 mr = 4 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4630 time to turn everything in is 1.940000 number of dielectric boundary points 77552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 17328 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) : 2.081344 object centre at (A) : 50.69400 43.05450 30.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1985170 0.8101367 midg,1,midg; midg,igrid,midg 0.1870880 -0.2326006 1,midg,midg; igrid,midg,midg 0.2159308 -3.1335495E-02 gauss-seidel spectral radius is 0.9993060 estimated iterations to convergence 299 setup time was (sec) 2.240000 now iterating at: 18:45:25 rms-change max change #iterations 10.63385 528.3335 at 10iterations 6.315650 120.5811 at 20iterations 3.743606 85.26880 at 30iterations 2.217365 43.40068 at 40iterations 1.302817 24.98253 at 50iterations 0.7683073 13.50775 at 60iterations 0.4521737 8.586220 at 70iterations 0.2649561 5.695719 at 80iterations 0.1553634 2.570399 at 90iterations 9.0971082E-02 1.681011 at 100iterations 5.3388540E-02 0.9358902 at 110iterations 3.1272851E-02 0.5216212 at 120iterations 1.8285746E-02 0.3240891 at 130iterations 1.0706213E-02 0.1846771 at 140iterations 6.2794341E-03 0.1102905 at 150iterations 3.6688680E-03 6.3765049E-02 at 160iterations 2.1483505E-03 3.9875031E-02 at 170iterations 1.2584577E-03 2.1886826E-02 at 180iterations finished qdiffx linear iterations at : 18:45:35 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 1.2584577E-03 2.1886826E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 18:45:35 12.607u 0.168s 0:13.09 97.4% 0+0k 0+0io 0pf+0w