Sat Oct 15 15:25:27 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+sph2.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 = amb2.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 15 2011 at 15:25:27 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6417884 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 0.6417884 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.154013 assigned positive charge : 414.8358 centred at (gu) : 90.35183 90.34950 91.85565 assigned negative charge : -412.6823 centred at (gu) : 90.10509 90.18584 91.76276 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7315 nv = 96 ne = 84 npr = 56702 no. pairs analyzed = 56702 no. exposed pairs = 3230 no. arc points = 22106 no. surface atoms = 1091 nbur = 1646 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 4179 m= 5 mr = 53 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 0.2100000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2196 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1764212E-09 2.2211090E-08 midg,1,midg; midg,igrid,midg -1.7348196E-08 2.5634955E-08 1,midg,midg; igrid,midg,midg -2.7784052E-08 3.6781223E-08 gauss-seidel spectral radius is 0.9874252 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 15:25:28 rms-change max change #iterations 0.1526057 19.44872 at 10iterations 1.5522645E-02 2.182932 at 20iterations 1.6327132E-03 0.2226868 at 30iterations 2.0177946E-04 2.7582169E-02 at 40iterations 3.5824851E-05 5.0106049E-03 at 50iterations finished qdiffx linear iterations at : 15:25:31 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 3.5824851E-05 5.0106049E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 15:25:31 3.877u 0.257s 0:04.45 92.5% 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 15 2011 at 15:25:31 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.925365 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 1.925365 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.154013 assigned positive charge : 414.8358 centred at (gu) : 91.05518 91.04770 95.56631 assigned negative charge : -412.6823 centred at (gu) : 90.31503 90.55733 95.28808 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22106 grid for indexing accessible points = 1.400000 m= 29043 mr = 55949 m= 4614 mr = 21840 m= 297 mr = 2991 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 614 time to turn everything in is 0.4100000 number of dielectric boundary points 32044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20342 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) : 0.6417884 object centre at (A) : 12.67500 -1.554500 17.34700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1558226E-02 1.2346609E-02 midg,1,midg; midg,igrid,midg -1.1432157E-02 2.6948504E-02 1,midg,midg; igrid,midg,midg -1.0234734E-02 6.0089927E-02 gauss-seidel spectral radius is 0.9986700 estimated iterations to convergence 217 setup time was (sec) 0.6700000 now iterating at: 15:25:32 rms-change max change #iterations 4.515407 246.3248 at 10iterations 2.135191 71.71595 at 20iterations 1.010929 31.01689 at 30iterations 0.4805560 15.33703 at 40iterations 0.2268025 8.044173 at 50iterations 0.1078232 3.521267 at 60iterations 5.1149812E-02 1.695320 at 70iterations 2.4213273E-02 0.7601479 at 80iterations 1.1488840E-02 0.3930359 at 90iterations 5.4523409E-03 0.1590433 at 100iterations 2.5897950E-03 8.0036163E-02 at 110iterations 1.2329386E-03 3.8068771E-02 at 120iterations finished qdiffx linear iterations at : 15:25:41 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 1.2329386E-03 3.8068771E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 15:25:41 9.135u 0.288s 0:09.69 97.1% 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 15 2011 at 15:25:41 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.888047 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 2.888047 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.154013 assigned positive charge : 414.8358 centred at (gu) : 91.58254 91.57159 98.34945 assigned negative charge : -412.6823 centred at (gu) : 90.47242 90.83600 97.93213 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 182593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22106 grid for indexing accessible points = 1.400000 m= 93999 mr = 135126 m= 34119 mr = 77810 m= 8336 mr = 27846 m= 1296 mr = 6474 m= 79 mr = 868 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1965 time to turn everything in is 1.110000 number of dielectric boundary points 72271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 20670 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) : 1.925365 object centre at (A) : 12.67500 -1.554500 17.34700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7295727 0.3913676 midg,1,midg; midg,igrid,midg -0.1071286 0.3328807 1,midg,midg; igrid,midg,midg -6.1241023E-02 0.5101486 gauss-seidel spectral radius is 0.9992632 estimated iterations to convergence 291 setup time was (sec) 1.400000 now iterating at: 15:25:43 rms-change max change #iterations 10.46261 385.0803 at 10iterations 6.097400 135.3965 at 20iterations 3.561125 75.51587 at 30iterations 2.066330 43.21637 at 40iterations 1.197192 23.19784 at 50iterations 0.6935726 11.91414 at 60iterations 0.4015708 6.782211 at 70iterations 0.2322579 4.188843 at 80iterations 0.1340359 2.400852 at 90iterations 7.7416524E-02 1.329028 at 100iterations 4.4662595E-02 0.7550821 at 110iterations 2.5760563E-02 0.4669476 at 120iterations 1.4880208E-02 0.2869892 at 130iterations 8.6077433E-03 0.1698608 at 140iterations 4.9846200E-03 8.7439775E-02 at 150iterations 2.8904600E-03 5.8164597E-02 at 160iterations 1.6864548E-03 3.1700134E-02 at 170iterations 9.9077134E-04 1.8024445E-02 at 180iterations finished qdiffx linear iterations at : 15:25:56 total time elapsed so far: 14.86000 # loops : 180 mean,max change (kT/e) : 9.9077134E-04 1.8024445E-02 energy calculations done at 14.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.99000 DelPhi exited at 15:25:57 14.992u 0.297s 0:15.66 97.5% 0+0k 0+0io 0pf+0w