Sun Oct 9 12:29:10 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 Sun Oct 9 2011 at 12:29:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: GLM 235 has a net charge of -0.0940 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: 0.7095166 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 0.7095166 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2213 net assigned charge : 3.406014 assigned positive charge : 360.4712 centred at (gu) : 89.22096 91.09763 90.66090 assigned negative charge : -357.0656 centred at (gu) : 89.24408 91.27911 90.69176 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 47855 no. pairs analyzed = 47855 no. exposed pairs = 2905 no. arc points = 20097 no. surface atoms = 972 nbur = 1386 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 511 mr = 4522 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.3000000 number of dielectric boundary points 3905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8958 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3846054E-08 1.4874532E-08 midg,1,midg; midg,igrid,midg 1.1055058E-07 -9.7367582E-08 1,midg,midg; igrid,midg,midg 5.2507708E-08 1.5549910E-08 gauss-seidel spectral radius is 0.9896723 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 12:29:11 rms-change max change #iterations 0.2200279 28.53144 at 10iterations 2.7426355E-02 3.759071 at 20iterations 3.5091741E-03 0.5156765 at 30iterations 5.1053159E-04 7.8697205E-02 at 40iterations 1.0000794E-04 1.6237259E-02 at 50iterations finished qdiffx linear iterations at : 12:29:13 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.0000794E-04 1.6237259E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 12:29:14 3.103u 0.145s 0:03.52 92.0% 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 Sun Oct 9 2011 at 12:29:14 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: GLM 235 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.128550 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 2.128550 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2213 net assigned charge : 3.406014 assigned positive charge : 360.4712 centred at (gu) : 87.66228 93.29235 91.98233 assigned negative charge : -357.0656 centred at (gu) : 87.73201 93.83709 92.07502 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 84381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20097 grid for indexing accessible points = 1.400000 m= 32398 mr = 59071 m= 5928 mr = 24233 m= 599 mr = 3877 m= 14 mr = 346 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2909 time to turn everything in is 0.6600000 number of dielectric boundary points 35793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17574 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) : 0.7095166 object centre at (A) : 19.31000 11.20650 23.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3456213E-02 1.1381763E-02 midg,1,midg; midg,igrid,midg 2.5324123E-02 -6.1881274E-02 1,midg,midg; igrid,midg,midg 5.9061695E-02 -1.1683088E-02 gauss-seidel spectral radius is 0.9988672 estimated iterations to convergence 235 setup time was (sec) 0.9100000 now iterating at: 12:29:15 rms-change max change #iterations 5.042021 221.1821 at 10iterations 2.511701 87.68776 at 20iterations 1.254539 39.33828 at 30iterations 0.6292177 18.81409 at 40iterations 0.3157703 9.395415 at 50iterations 0.1579938 4.383015 at 60iterations 7.9191133E-02 2.202175 at 70iterations 3.9721459E-02 1.095219 at 80iterations 2.0004831E-02 0.6654022 at 90iterations 1.0063902E-02 0.2804642 at 100iterations 5.0551221E-03 0.1503849 at 110iterations 2.5667464E-03 7.0275307E-02 at 120iterations finished qdiffx linear iterations at : 12:29:21 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 2.5667464E-03 7.0275307E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 12:29:22 7.243u 0.182s 0:07.76 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 Sun Oct 9 2011 at 12:29:22 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: GLM 235 has a net charge of -0.0940 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: 3.192825 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 3.192825 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2213 net assigned charge : 3.406014 assigned positive charge : 360.4712 centred at (gu) : 86.49356 94.93855 92.97334 assigned negative charge : -357.0656 centred at (gu) : 86.59795 95.75562 93.11240 start vw surface at 0.1700000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 194732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20097 grid for indexing accessible points = 1.400000 m= 102513 mr = 142847 m= 39821 mr = 84485 m= 11096 mr = 32318 m= 2320 mr = 8613 m= 346 mr = 1744 m= 12 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 10155 time to turn everything in is 1.880000 number of dielectric boundary points 80585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 17703 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) : 2.128550 object centre at (A) : 19.31000 11.20650 23.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4996584 -7.9422714E-03 midg,1,midg; midg,igrid,midg 0.5542158 -0.6226007 1,midg,midg; igrid,midg,midg 0.5894822 -0.4121597 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 2.160000 now iterating at: 12:29:24 rms-change max change #iterations 11.13333 485.6810 at 10iterations 6.604630 127.7359 at 20iterations 3.911969 71.18390 at 30iterations 2.304850 39.42569 at 40iterations 1.360409 21.64897 at 50iterations 0.8033582 13.85914 at 60iterations 0.4724217 8.528950 at 70iterations 0.2776056 4.604996 at 80iterations 0.1632823 2.867966 at 90iterations 9.6013285E-02 1.663209 at 100iterations 5.6357048E-02 0.9637833 at 110iterations 3.3217117E-02 0.5310593 at 120iterations 1.9634547E-02 0.3388443 at 130iterations 1.1658059E-02 0.1987724 at 140iterations 7.0164609E-03 0.1209793 at 150iterations 4.3010917E-03 7.6530457E-02 at 160iterations 2.7212368E-03 5.4199219E-02 at 170iterations 1.8039555E-03 3.4141541E-02 at 180iterations finished qdiffx linear iterations at : 12:29:33 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 1.8039555E-03 3.4141541E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 12:29:34 11.767u 0.167s 0:12.21 97.6% 0+0k 0+0io 0pf+0w