Wed Dec 21 14:21:07 PST 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 Wed Dec 21 2011 at 14:21:07 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 = 1964 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: 0.6446939 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 0.6446939 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.77703 92.62135 90.13818 assigned negative charge : -285.8263 centred at (gu) : 90.90397 92.78191 90.07098 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 41181 no. pairs analyzed = 41181 no. exposed pairs = 2410 no. arc points = 16873 no. surface atoms = 818 nbur = 1146 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 260 mr = 3094 m= 0 mr = 33 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5751208E-09 1.0634282E-08 midg,1,midg; midg,igrid,midg 1.0993878E-08 -2.1416144E-08 1,midg,midg; igrid,midg,midg 1.3536286E-08 -1.0166846E-08 gauss-seidel spectral radius is 0.9874749 estimated iterations to convergence 73 setup time was (sec) 0.6300000 now iterating at: 14:21:08 rms-change max change #iterations 0.1255926 19.30881 at 10iterations 1.2568973E-02 2.083900 at 20iterations 1.2741628E-03 0.2057190 at 30iterations 1.2704721E-04 2.1926880E-02 at 40iterations 1.2612163E-05 2.0141602E-03 at 50iterations finished qdiffx linear iterations at : 14:21:12 total time elapsed so far: 5.010000 # loops : 50 mean,max change (kT/e) : 1.2612163E-05 2.0141602E-03 energy calculations done at 5.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 14:21:13 5.201u 0.425s 0:06.81 82.5% 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 Wed Dec 21 2011 at 14:21:14 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 = 1964 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: 1.934082 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 1.934082 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.33128 97.86409 90.41463 assigned negative charge : -285.8263 centred at (gu) : 92.71211 98.34604 90.21312 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16873 grid for indexing accessible points = 1.400000 m= 21549 mr = 41442 m= 3139 mr = 16300 m= 140 mr = 1941 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1239 time to turn everything in is 0.5600000 number of dielectric boundary points 24666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14435 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) : 0.6446939 object centre at (A) : 14.26450 22.10900 3.339001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9840680E-02 1.3014057E-02 midg,1,midg; midg,igrid,midg 3.0482950E-02 -1.8798554E-02 1,midg,midg; igrid,midg,midg 9.3611591E-03 -7.3599233E-03 gauss-seidel spectral radius is 0.9985945 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 14:21:15 rms-change max change #iterations 3.625134 179.2138 at 10iterations 1.679793 63.97684 at 20iterations 0.7779231 28.63260 at 30iterations 0.3619839 13.61481 at 40iterations 0.1669310 6.148434 at 50iterations 7.7224456E-02 2.597137 at 60iterations 3.5774022E-02 1.349360 at 70iterations 1.6621122E-02 0.6366386 at 80iterations 7.6751891E-03 0.2700748 at 90iterations 3.5528308E-03 0.1278820 at 100iterations 1.6479854E-03 5.5736065E-02 at 110iterations 7.6416356E-04 2.7865648E-02 at 120iterations finished qdiffx linear iterations at : 14:21:24 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 7.6416356E-04 2.7865648E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 14:21:27 10.143u 0.576s 0:13.52 79.2% 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 Wed Dec 21 2011 at 14:21:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.901123 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 2.901123 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 93.49680 101.7961 90.62189 assigned negative charge : -285.8263 centred at (gu) : 94.06821 102.5191 90.31965 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 137687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16873 grid for indexing accessible points = 1.400000 m= 70227 mr = 100206 m= 25037 mr = 58245 m= 5438 mr = 20593 m= 614 mr = 4007 m= 28 mr = 353 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4199 time to turn everything in is 1.460000 number of dielectric boundary points 55626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 14656 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) : 1.934082 object centre at (A) : 14.26450 22.10900 3.339001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9467329 1.1714402E-02 midg,1,midg; midg,igrid,midg 0.3078999 -0.1917114 1,midg,midg; igrid,midg,midg 4.8715021E-02 -4.5881391E-02 gauss-seidel spectral radius is 0.9992316 estimated iterations to convergence 285 setup time was (sec) 1.850000 now iterating at: 14:21:30 rms-change max change #iterations 8.569096 419.4704 at 10iterations 4.922131 120.7813 at 20iterations 2.804287 66.13992 at 30iterations 1.590766 35.59147 at 40iterations 0.9085842 18.14402 at 50iterations 0.5153708 10.00395 at 60iterations 0.2930278 6.444277 at 70iterations 0.1666721 3.440357 at 80iterations 9.4448119E-02 1.924637 at 90iterations 5.3778153E-02 1.204955 at 100iterations 3.0502522E-02 0.6199093 at 110iterations 1.7250963E-02 0.3567190 at 120iterations 9.8177902E-03 0.1920490 at 130iterations 5.5595273E-03 0.1048212 at 140iterations 3.1581973E-03 6.1252594E-02 at 150iterations 1.7962264E-03 3.5614014E-02 at 160iterations 1.0189627E-03 2.0618439E-02 at 170iterations 5.7792122E-04 1.1398315E-02 at 180iterations finished qdiffx linear iterations at : 14:21:46 total time elapsed so far: 18.34000 # loops : 180 mean,max change (kT/e) : 5.7792122E-04 1.1398315E-02 energy calculations done at 18.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 14:21:50 18.545u 0.476s 0:22.92 82.9% 0+0k 0+0io 0pf+0w