Sun Oct 9 13:09:24 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 13:09:24 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 = 2353 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: 0.6797266 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 0.6797266 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 358.2111 centred at (gu) : 89.39204 90.95823 90.84683 assigned negative charge : -354.7116 centred at (gu) : 89.39210 91.13309 90.92216 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7578 nv = 96 ne = 84 npr = 45724 no. pairs analyzed = 45724 no. exposed pairs = 2997 no. arc points = 21169 no. surface atoms = 1016 nbur = 1337 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4214 m= 6 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2079 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1856498E-08 -8.0934699E-09 midg,1,midg; midg,igrid,midg 5.4636551E-08 -4.5077094E-08 1,midg,midg; igrid,midg,midg 1.7757287E-08 1.3968639E-08 gauss-seidel spectral radius is 0.9887626 estimated iterations to convergence 77 setup time was (sec) 0.4900000 now iterating at: 13:09:25 rms-change max change #iterations 0.1793406 25.25555 at 10iterations 2.0436034E-02 2.584310 at 20iterations 2.6941239E-03 0.3105192 at 30iterations 5.1237689E-04 6.7131042E-02 at 40iterations 1.4264382E-04 1.7084122E-02 at 50iterations finished qdiffx linear iterations at : 13:09:27 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.4264382E-04 1.7084122E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 13:09:28 3.075u 0.128s 0:03.51 90.8% 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 13:09:28 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 = 2353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.039180 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 2.039180 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 358.2111 centred at (gu) : 88.17577 92.87422 92.53978 assigned negative charge : -354.7116 centred at (gu) : 88.17606 93.39909 92.76632 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 81000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21169 grid for indexing accessible points = 1.400000 m= 32276 mr = 56201 m= 5779 mr = 24498 m= 487 mr = 3772 m= 11 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 392 time to turn everything in is 0.5500000 number of dielectric boundary points 34874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17515 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) : 0.6797266 object centre at (A) : 19.20100 11.57700 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0804207E-02 7.8609921E-03 midg,1,midg; midg,igrid,midg 1.8544659E-02 -6.1237730E-02 1,midg,midg; igrid,midg,midg 4.3694012E-02 -1.0890502E-02 gauss-seidel spectral radius is 0.9987862 estimated iterations to convergence 227 setup time was (sec) 0.8100000 now iterating at: 13:09:28 rms-change max change #iterations 4.613114 212.6637 at 10iterations 2.239403 81.02744 at 20iterations 1.096892 36.56609 at 30iterations 0.5348915 16.33609 at 40iterations 0.2616894 7.705971 at 50iterations 0.1281944 4.162817 at 60iterations 6.2826917E-02 1.964836 at 70iterations 3.0899160E-02 0.9435868 at 80iterations 1.5196690E-02 0.4621048 at 90iterations 7.4928529E-03 0.2259779 at 100iterations 3.7459014E-03 0.1110229 at 110iterations 1.9069009E-03 5.3588867E-02 at 120iterations finished qdiffx linear iterations at : 13:09:34 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.9069009E-03 5.3588867E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 13:09:35 6.943u 0.168s 0:07.39 96.0% 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 Sun Oct 9 2011 at 13:09:35 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 = 2353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.058770 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): -6.097000 44.49900 ymin,ymax (A): -14.61000 37.76400 zmin,zma (A): 1.151000 45.90700 x,y,z range (A): 50.59600 52.37400 44.75600 scale (grids/A): 3.058770 object centre (A): 19.20100 11.57700 23.52900 number of atom coordinates read : 2353 total number of charged atoms : 2212 net assigned charge : 3.500019 assigned positive charge : 358.2111 centred at (gu) : 87.26355 94.31128 93.80965 assigned negative charge : -354.7116 centred at (gu) : 87.26397 95.09863 94.14945 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21169 grid for indexing accessible points = 1.400000 m= 101085 mr = 135929 m= 40350 mr = 83677 m= 10648 mr = 33141 m= 1890 mr = 8147 m= 198 mr = 1312 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1545 time to turn everything in is 1.500000 number of dielectric boundary points 78690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 17694 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) : 2.039180 object centre at (A) : 19.20100 11.57700 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3951473 -3.2375205E-02 midg,1,midg; midg,igrid,midg 0.4535390 -0.7466307 1,midg,midg; igrid,midg,midg 0.4595657 -0.3566658 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 1.770000 now iterating at: 13:09:37 rms-change max change #iterations 10.57750 433.8244 at 10iterations 6.273647 134.0603 at 20iterations 3.703205 68.31383 at 30iterations 2.186470 39.04086 at 40iterations 1.288400 24.11491 at 50iterations 0.7583694 13.88806 at 60iterations 0.4430919 7.878170 at 70iterations 0.2591273 4.732896 at 80iterations 0.1520985 2.721328 at 90iterations 8.9025997E-02 1.650443 at 100iterations 5.1904812E-02 0.8895321 at 110iterations 3.0404711E-02 0.5233765 at 120iterations 1.7875593E-02 0.3110809 at 130iterations 1.0553634E-02 0.2043762 at 140iterations 6.3106730E-03 0.1090469 at 150iterations 3.8335677E-03 7.4779510E-02 at 160iterations 2.4123888E-03 5.1876068E-02 at 170iterations 1.5835159E-03 3.3660889E-02 at 180iterations finished qdiffx linear iterations at : 13:09:46 total time elapsed so far: 11.23000 # loops : 180 mean,max change (kT/e) : 1.5835159E-03 3.3660889E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 13:09:47 11.415u 0.172s 0:11.86 97.6% 0+0k 0+0io 0pf+0w