Sat Oct 8 20:36:35 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 Sat Oct 8 2011 at 20:36:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6256590 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 0.6256590 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 88.49371 89.22861 89.65688 assigned negative charge : -387.9975 centred at (gu) : 88.40177 89.27541 89.55647 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6669 nv = 96 ne = 84 npr = 52294 no. pairs analyzed = 52294 no. exposed pairs = 3034 no. arc points = 21693 no. surface atoms = 1022 nbur = 1543 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3762 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2900000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3088670E-09 1.0835839E-08 midg,1,midg; midg,igrid,midg 8.9527052E-09 2.5911129E-10 1,midg,midg; igrid,midg,midg -4.7288720E-09 7.9609741E-09 gauss-seidel spectral radius is 0.9867642 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 20:36:35 rms-change max change #iterations 0.1328607 18.79917 at 10iterations 1.2640192E-02 1.852818 at 20iterations 1.1748235E-03 0.1777573 at 30iterations 1.1427188E-04 1.6613007E-02 at 40iterations 1.0995614E-05 1.5811920E-03 at 50iterations finished qdiffx linear iterations at : 20:36:38 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.0995614E-05 1.5811920E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 20:36:38 3.346u 0.199s 0:03.82 92.4% 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 Sat Oct 8 2011 at 20:36:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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: 1.876977 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 1.876977 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 85.48061 87.68559 88.97015 assigned negative charge : -387.9975 centred at (gu) : 85.20501 87.82593 88.66915 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21693 grid for indexing accessible points = 1.400000 m= 26329 mr = 50808 m= 3854 mr = 19782 m= 189 mr = 2344 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2585 time to turn everything in is 0.5200000 number of dielectric boundary points 29867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19314 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) : 0.6256590 object centre at (A) : -7.121500 -0.3210001 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3233976E-02 2.3007773E-02 midg,1,midg; midg,igrid,midg 1.3306540E-02 3.4707591E-03 1,midg,midg; igrid,midg,midg -8.3858101E-04 3.2380208E-02 gauss-seidel spectral radius is 0.9985918 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 20:36:40 rms-change max change #iterations 4.101038 203.7905 at 10iterations 1.905936 67.80651 at 20iterations 0.8844272 30.87143 at 30iterations 0.4083428 14.08436 at 40iterations 0.1897770 6.476792 at 50iterations 8.8017292E-02 2.896126 at 60iterations 4.0799890E-02 1.532223 at 70iterations 1.8895380E-02 0.6767416 at 80iterations 8.7606590E-03 0.2803478 at 90iterations 4.0507866E-03 0.1288805 at 100iterations 1.8765611E-03 5.7188511E-02 at 110iterations 8.6946465E-04 3.0379295E-02 at 120iterations finished qdiffx linear iterations at : 20:36:46 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 8.6946465E-04 3.0379295E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 20:36:47 7.575u 0.225s 0:08.08 96.4% 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 Sat Oct 8 2011 at 20:36:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 465 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: 2.815466 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): -31.88200 17.63900 ymin,ymax (A): -23.93900 23.29700 zmin,zma (A): -12.15900 44.74100 x,y,z range (A): 49.52100 47.23600 56.90000 scale (grids/A): 2.815466 object centre (A): -7.121500 -0.3210001 16.29100 number of atom coordinates read : 2565 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 83.22093 86.52818 88.45502 assigned negative charge : -387.9975 centred at (gu) : 82.80743 86.73880 88.00365 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 167346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21693 grid for indexing accessible points = 1.400000 m= 86038 mr = 122606 m= 30529 mr = 71413 m= 6834 mr = 24666 m= 838 mr = 5046 m= 45 mr = 525 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 9301 time to turn everything in is 1.280000 number of dielectric boundary points 67358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19651 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) : 1.876977 object centre at (A) : -7.121500 -0.3210001 16.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3464131E-02 0.2528026 midg,1,midg; midg,igrid,midg 0.1715847 3.4586627E-02 1,midg,midg; igrid,midg,midg 1.2034388E-02 0.4205532 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.590000 now iterating at: 20:36:49 rms-change max change #iterations 9.627622 304.2604 at 10iterations 5.559705 117.6719 at 20iterations 3.185241 61.99419 at 30iterations 1.829251 40.25176 at 40iterations 1.047730 25.61887 at 50iterations 0.5986507 12.51709 at 60iterations 0.3422661 6.276905 at 70iterations 0.1955153 3.487514 at 80iterations 0.1117263 2.422882 at 90iterations 6.3748777E-02 1.214740 at 100iterations 3.6403760E-02 0.7204151 at 110iterations 2.0740839E-02 0.3846006 at 120iterations 1.1858412E-02 0.2098083 at 130iterations 6.7759147E-03 0.1336212 at 140iterations 3.8604876E-03 7.0190430E-02 at 150iterations 2.2080112E-03 4.0807724E-02 at 160iterations 1.2583111E-03 2.2954941E-02 at 170iterations 7.2018220E-04 1.3805389E-02 at 180iterations finished qdiffx linear iterations at : 20:36:59 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 7.2018220E-04 1.3805389E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 20:36:59 12.195u 0.253s 0:12.72 97.7% 0+0k 0+0io 0pf+0w