Mon Oct 10 00:33:33 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 00:33:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 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: 0.6131799 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 0.6131799 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.5316 centred at (gu) : 89.51624 89.63943 91.58368 assigned negative charge : -449.9321 centred at (gu) : 89.39409 89.84705 91.76392 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7389 nv = 96 ne = 84 npr = 62513 no. pairs analyzed = 62513 no. exposed pairs = 3593 no. arc points = 24777 no. surface atoms = 1216 nbur = 1773 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 4140 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3500000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2458 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1101690E-09 -2.5846747E-08 midg,1,midg; midg,igrid,midg 6.7673018E-09 -1.8369212E-08 1,midg,midg; igrid,midg,midg -1.5950846E-08 8.9110552E-10 gauss-seidel spectral radius is 0.9862610 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 00:33:34 rms-change max change #iterations 0.1308812 20.83928 at 10iterations 1.2240795E-02 1.917568 at 20iterations 1.2731226E-03 0.2707024 at 30iterations 3.1101788E-04 6.5731049E-02 at 40iterations 1.2594416E-04 2.6094437E-02 at 50iterations finished qdiffx linear iterations at : 00:33:36 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.2594416E-04 2.6094437E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 00:33:37 3.461u 0.168s 0:03.92 92.3% 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 00:33:37 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.839540 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 1.839540 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.5316 centred at (gu) : 88.54803 88.91775 94.75050 assigned negative charge : -449.9321 centred at (gu) : 88.18195 89.54069 95.29141 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24777 grid for indexing accessible points = 1.400000 m= 28718 mr = 57221 m= 4342 mr = 20990 m= 252 mr = 2623 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 0.6200000 number of dielectric boundary points 33360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22362 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) : 0.6131799 object centre at (A) : 38.44200 -12.74950 3.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2974769E-02 -6.1582316E-02 midg,1,midg; midg,igrid,midg 5.1543219E-03 -2.3058482E-02 1,midg,midg; igrid,midg,midg -4.2050071E-02 -2.4886798E-02 gauss-seidel spectral radius is 0.9985743 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 00:33:38 rms-change max change #iterations 4.241526 157.6637 at 10iterations 1.950077 60.10220 at 20iterations 0.9019920 28.19335 at 30iterations 0.4143390 12.18438 at 40iterations 0.1906072 6.658508 at 50iterations 8.7845773E-02 2.687715 at 60iterations 4.0472064E-02 1.406631 at 70iterations 1.8762898E-02 0.6141397 at 80iterations 8.6630024E-03 0.2529116 at 90iterations 4.0327101E-03 0.1214771 at 100iterations 1.8967026E-03 5.6322098E-02 at 110iterations 9.1685972E-04 3.0706406E-02 at 120iterations finished qdiffx linear iterations at : 00:33:45 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 9.1685972E-04 3.0706406E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 00:33:45 8.095u 0.197s 0:08.66 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 00:33:45 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIY 166 has a net charge of 0.2000 !!! WARNING: ZN1 1086 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.759310 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): 9.412999 67.47100 ymin,ymax (A): -37.19700 11.69800 zmin,zma (A): -22.95900 29.13800 x,y,z range (A): 58.05800 48.89500 52.09700 scale (grids/A): 2.759310 object centre (A): 38.44200 -12.74950 3.089500 number of atom coordinates read : 2989 total number of charged atoms : 2851 net assigned charge : -10.39998 assigned positive charge : 439.5316 centred at (gu) : 87.82188 88.37646 97.12585 assigned negative charge : -449.9321 centred at (gu) : 87.27278 89.31102 97.93716 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 187508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24777 grid for indexing accessible points = 1.400000 m= 94011 mr = 138642 m= 33246 mr = 77105 m= 7599 mr = 26298 m= 1053 mr = 5534 m= 56 mr = 696 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 5135 time to turn everything in is 1.610000 number of dielectric boundary points 75177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 22807 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) : 1.839540 object centre at (A) : 38.44200 -12.74950 3.089500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3657492 -0.6894326 midg,1,midg; midg,igrid,midg 5.8896422E-02 -0.1336050 1,midg,midg; igrid,midg,midg -0.4145339 -0.3716739 gauss-seidel spectral radius is 0.9992443 estimated iterations to convergence 287 setup time was (sec) 1.940000 now iterating at: 00:33:48 rms-change max change #iterations 10.08275 310.0320 at 10iterations 5.866969 120.9954 at 20iterations 3.387355 66.51170 at 30iterations 1.952609 39.18317 at 40iterations 1.121222 22.00100 at 50iterations 0.6442724 12.70274 at 60iterations 0.3693651 6.841511 at 70iterations 0.2119301 3.865980 at 80iterations 0.1214090 2.345411 at 90iterations 6.9379203E-02 1.221724 at 100iterations 3.9704587E-02 0.7677221 at 110iterations 2.2712171E-02 0.3824644 at 120iterations 1.3030843E-02 0.2258263 at 130iterations 7.4666417E-03 0.1363828 at 140iterations 4.2733480E-03 7.4707031E-02 at 150iterations 2.4468084E-03 4.1253328E-02 at 160iterations 1.4016227E-03 2.4192810E-02 at 170iterations 8.0924085E-04 1.3294220E-02 at 180iterations finished qdiffx linear iterations at : 00:33:59 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 8.0924085E-04 1.3294220E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 00:33:59 13.373u 0.218s 0:13.87 97.9% 0+0k 0+0io 0pf+0w