Sun Oct 9 14:06:02 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 14:06:02 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2422 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: 0.6800382 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): -7.162000 42.04000 ymin,ymax (A): -2.688000 49.66200 zmin,zma (A): -5.278000 36.82600 x,y,z range (A): 49.20200 52.35000 42.10400 scale (grids/A): 0.6800382 object centre (A): 17.43900 23.48700 15.77400 number of atom coordinates read : 2422 total number of charged atoms : 2279 net assigned charge : 4.500029 assigned positive charge : 375.5670 centred at (gu) : 90.68132 89.37405 89.20285 assigned negative charge : -371.0675 centred at (gu) : 90.64497 89.22173 89.07894 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7472 nv = 96 ne = 84 npr = 48516 no. pairs analyzed = 48516 no. exposed pairs = 3041 no. arc points = 21253 no. surface atoms = 1018 nbur = 1404 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4147 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1988 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2668511E-08 4.9413508E-08 midg,1,midg; midg,igrid,midg -3.2180676E-08 5.8691715E-08 1,midg,midg; igrid,midg,midg 7.6603808E-09 3.5836397E-08 gauss-seidel spectral radius is 0.9887689 estimated iterations to convergence 77 setup time was (sec) 0.4000000 now iterating at: 14:06:02 rms-change max change #iterations 0.1873547 27.07911 at 10iterations 2.2064906E-02 3.256353 at 20iterations 3.0946573E-03 0.5162430 at 30iterations 6.9306121E-04 0.1055069 at 40iterations 2.1267982E-04 3.3676147E-02 at 50iterations finished qdiffx linear iterations at : 14:06:05 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.1267982E-04 3.3676147E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:06:06 3.395u 0.168s 0:03.85 92.2% 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 Sun Oct 9 2011 at 14:06:06 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2422 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: 2.040115 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): -7.162000 42.04000 ymin,ymax (A): -2.688000 49.66200 zmin,zma (A): -5.278000 36.82600 x,y,z range (A): 49.20200 52.35000 42.10400 scale (grids/A): 2.040115 object centre (A): 17.43900 23.48700 15.77400 number of atom coordinates read : 2422 total number of charged atoms : 2279 net assigned charge : 4.500029 assigned positive charge : 375.5670 centred at (gu) : 92.04327 88.12164 87.60776 assigned negative charge : -371.0675 centred at (gu) : 91.93462 87.66508 87.23671 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21253 grid for indexing accessible points = 1.400000 m= 30541 mr = 55752 m= 5264 mr = 22615 m= 480 mr = 3299 m= 6 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18066 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) : 0.6800382 object centre at (A) : 17.43900 23.48700 15.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9946375E-03 5.1849242E-02 midg,1,midg; midg,igrid,midg -5.1274810E-02 1.3702767E-02 1,midg,midg; igrid,midg,midg 3.6242172E-02 1.3647616E-02 gauss-seidel spectral radius is 0.9987839 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 14:06:06 rms-change max change #iterations 4.769561 216.2968 at 10iterations 2.320811 92.03385 at 20iterations 1.135229 36.45788 at 30iterations 0.5573737 17.13011 at 40iterations 0.2716891 8.481895 at 50iterations 0.1332756 3.929828 at 60iterations 6.5307401E-02 2.043575 at 70iterations 3.2078668E-02 0.9324265 at 80iterations 1.5957456E-02 0.4608154 at 90iterations 8.0059553E-03 0.2519588 at 100iterations 4.0904665E-03 0.1160965 at 110iterations 2.1732869E-03 6.5086365E-02 at 120iterations finished qdiffx linear iterations at : 14:06:14 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.1732869E-03 6.5086365E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:06:14 7.843u 0.203s 0:08.32 96.6% 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 14:06:14 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2422 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: 3.060172 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): -7.162000 42.04000 ymin,ymax (A): -2.688000 49.66200 zmin,zma (A): -5.278000 36.82600 x,y,z range (A): 49.20200 52.35000 42.10400 scale (grids/A): 3.060172 object centre (A): 17.43900 23.48700 15.77400 number of atom coordinates read : 2422 total number of charged atoms : 2279 net assigned charge : 4.500029 assigned positive charge : 375.5670 centred at (gu) : 93.06490 87.18238 86.41160 assigned negative charge : -371.0675 centred at (gu) : 92.90183 86.49756 85.85500 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21253 grid for indexing accessible points = 1.400000 m= 96556 mr = 134622 m= 37086 mr = 79301 m= 9698 mr = 29967 m= 1850 mr = 7180 m= 236 mr = 1367 m= 1 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 77007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18232 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) : 2.040115 object centre at (A) : 17.43900 23.48700 15.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8628109E-02 0.4958178 midg,1,midg; midg,igrid,midg -0.6603683 0.2061304 1,midg,midg; igrid,midg,midg 0.4439058 -8.3837181E-02 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 1.280000 now iterating at: 14:06:16 rms-change max change #iterations 10.80304 371.2109 at 10iterations 6.362633 152.8457 at 20iterations 3.752595 71.36256 at 30iterations 2.203646 43.03905 at 40iterations 1.294420 23.79356 at 50iterations 0.7603871 14.48467 at 60iterations 0.4438514 7.662872 at 70iterations 0.2599202 4.814430 at 80iterations 0.1515822 2.613873 at 90iterations 8.9012064E-02 1.617464 at 100iterations 5.2074987E-02 0.9032364 at 110iterations 3.0640190E-02 0.5467930 at 120iterations 1.8145122E-02 0.3265228 at 130iterations 1.0976189E-02 0.2199135 at 140iterations 6.8046330E-03 0.1373062 at 150iterations 4.4194818E-03 9.6197605E-02 at 160iterations 3.0382969E-03 6.3991547E-02 at 170iterations 2.2164364E-03 4.8343658E-02 at 180iterations finished qdiffx linear iterations at : 14:06:27 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.2164364E-03 4.8343658E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 14:06:27 12.867u 0.206s 0:13.34 97.9% 0+0k 0+0io 0pf+0w