Mon Oct 10 16:13:18 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 16:13:19 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 = 4762 !!! WARNING: ASP 606 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5518097 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 0.5518097 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4604 net assigned charge : 6.000028 assigned positive charge : 718.5736 centred at (gu) : 90.36957 89.95185 88.40806 assigned negative charge : -712.5781 centred at (gu) : 90.41476 89.98051 88.40221 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9280 nv = 96 ne = 84 npr = 98207 no. pairs analyzed = 98207 no. exposed pairs = 5768 no. arc points = 39005 no. surface atoms = 1941 nbur = 2821 mkacc time = 0.2700000 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 = 1.568000 m= 366 mr = 5164 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3990 ## 537 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 12286 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7435440E-10 3.7528292E-10 midg,1,midg; midg,igrid,midg 8.5682150E-10 9.0631891E-11 1,midg,midg; igrid,midg,midg 9.7131747E-10 -1.4326615E-10 gauss-seidel spectral radius is 0.9831922 estimated iterations to convergence 63 setup time was (sec) 0.8500000 now iterating at: 16:13:20 rms-change max change #iterations 9.9404246E-02 13.48640 at 10iterations 7.4364240E-03 1.013523 at 20iterations 1.2159760E-03 0.2145348 at 30iterations 4.6281816E-04 7.1422577E-02 at 40iterations 2.0040704E-04 2.6374817E-02 at 50iterations finished qdiffx linear iterations at : 16:13:23 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 2.0040704E-04 2.6374817E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 16:13:24 4.395u 0.243s 0:05.43 85.2% 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 16:13:24 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 = 4762 !!! WARNING: ASP 606 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.655429 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 1.655429 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4604 net assigned charge : 6.000028 assigned positive charge : 718.5736 centred at (gu) : 91.10728 89.85399 85.22264 assigned negative charge : -712.5781 centred at (gu) : 91.24399 89.94068 85.20616 start vw surface at 0.2300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 103997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33174 mr = 74089 m= 3516 mr = 23377 m= 104 mr = 1725 m= 0 mr = 17 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 999 time to turn everything in is 0.8800000 number of dielectric boundary points 41583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 415 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 35363 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) : 0.5518097 object centre at (A) : 3.885000 -2.568002 3.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4937040E-02 -5.5716909E-03 midg,1,midg; midg,igrid,midg 1.6562819E-02 1.9647967E-02 1,midg,midg; igrid,midg,midg 6.8965447E-03 9.9516416E-04 gauss-seidel spectral radius is 0.9984054 estimated iterations to convergence 199 setup time was (sec) 1.220000 now iterating at: 16:13:26 rms-change max change #iterations 4.466804 217.0266 at 10iterations 1.975775 60.94220 at 20iterations 0.8682982 25.28469 at 30iterations 0.3830284 10.02691 at 40iterations 0.1689216 4.831646 at 50iterations 7.4492343E-02 2.060938 at 60iterations 3.3116374E-02 0.9419661 at 70iterations 1.4670219E-02 0.4461212 at 80iterations 6.6308668E-03 0.2043915 at 90iterations 3.0731848E-03 0.1051340 at 100iterations 1.5070743E-03 4.8420906E-02 at 110iterations 8.3324977E-04 2.8472900E-02 at 120iterations finished qdiffx linear iterations at : 16:13:35 total time elapsed so far: 9.780000 # loops : 120 mean,max change (kT/e) : 8.3324977E-04 2.8472900E-02 energy calculations done at 9.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 16:13:35 9.962u 0.256s 0:10.67 95.6% 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 16:13:35 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 = 4762 !!! WARNING: ASP 606 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.483144 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 2.483144 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4604 net assigned charge : 6.000028 assigned positive charge : 718.5736 centred at (gu) : 91.66064 89.78047 82.83349 assigned negative charge : -712.5781 centred at (gu) : 91.86599 89.91096 82.80896 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 242130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 115391 mr = 181079 m= 33386 mr = 92631 m= 5575 mr = 25419 m= 448 mr = 3699 m= 18 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 3389 time to turn everything in is 1.880000 number of dielectric boundary points 93900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 36782 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) : 1.655429 object centre at (A) : 3.885000 -2.568002 3.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4278135 -0.1090169 midg,1,midg; midg,igrid,midg 0.1740733 0.3721102 1,midg,midg; igrid,midg,midg 0.1104065 2.3010170E-02 gauss-seidel spectral radius is 0.9992419 estimated iterations to convergence 287 setup time was (sec) 2.230000 now iterating at: 16:13:38 rms-change max change #iterations 11.47939 363.2263 at 10iterations 6.761155 153.0973 at 20iterations 3.948848 90.25278 at 30iterations 2.304767 44.23888 at 40iterations 1.336098 26.21885 at 50iterations 0.7746614 15.18161 at 60iterations 0.4469898 7.903224 at 70iterations 0.2574530 4.876751 at 80iterations 0.1484928 2.820801 at 90iterations 8.5184932E-02 1.592410 at 100iterations 4.8947409E-02 0.7649708 at 110iterations 2.8104840E-02 0.4847481 at 120iterations 1.6160430E-02 0.3501892 at 130iterations 9.2934696E-03 0.1822777 at 140iterations 5.3614285E-03 9.5088959E-02 at 150iterations 3.1121932E-03 5.9701920E-02 at 160iterations 1.8253295E-03 3.0960083E-02 at 170iterations 1.0992520E-03 1.9119263E-02 at 180iterations finished qdiffx linear iterations at : 16:13:51 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 1.0992520E-03 1.9119263E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.25000 DelPhi exited at 16:13:52 16.247u 0.273s 0:16.79 98.3% 0+0k 0+0io 0pf+0w