Mon Oct 10 19:33:04 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 Mon Oct 10 2011 at 19:33:04 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 155 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5588697 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): 17.23000 64.38400 ymin,ymax (A): -9.664001 41.82200 zmin,zma (A): -1.423000 62.27700 x,y,z range (A): 47.15400 51.48600 63.70000 scale (grids/A): 0.5588697 object centre (A): 40.80700 16.07900 30.42700 number of atom coordinates read : 2588 total number of charged atoms : 2443 net assigned charge : 1.906022 assigned positive charge : 385.1130 centred at (gu) : 90.24431 89.30963 89.53812 assigned negative charge : -383.2077 centred at (gu) : 90.19743 89.22514 89.60231 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5346 nv = 96 ne = 84 npr = 51839 no. pairs analyzed = 51839 no. exposed pairs = 3482 no. arc points = 24706 no. surface atoms = 1156 nbur = 1432 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 201 mr = 2610 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2534 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7415947E-10 -3.5324432E-10 midg,1,midg; midg,igrid,midg -6.9782186E-10 8.1485074E-10 1,midg,midg; igrid,midg,midg -2.2149713E-10 6.6247541E-10 gauss-seidel spectral radius is 0.9834596 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 19:33:05 rms-change max change #iterations 7.5383514E-02 17.66821 at 10iterations 5.3223446E-03 1.031372 at 20iterations 3.7862040E-04 6.1660767E-02 at 30iterations 2.6587659E-05 5.3176880E-03 at 40iterations 1.9438103E-06 3.2424927E-04 at 50iterations finished qdiffx linear iterations at : 19:33:09 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 1.9438103E-06 3.2424927E-04 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 19:33:10 4.570u 0.374s 0:05.83 84.7% 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 Mon Oct 10 2011 at 19:33:10 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 155 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.676609 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): 17.23000 64.38400 ymin,ymax (A): -9.664001 41.82200 zmin,zma (A): -1.423000 62.27700 x,y,z range (A): 47.15400 51.48600 63.70000 scale (grids/A): 1.676609 object centre (A): 40.80700 16.07900 30.42700 number of atom coordinates read : 2588 total number of charged atoms : 2443 net assigned charge : 1.906022 assigned positive charge : 385.1130 centred at (gu) : 90.73231 87.92834 88.61436 assigned negative charge : -383.2077 centred at (gu) : 90.59212 87.67542 88.80684 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24706 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17500 mr = 38509 m= 1778 mr = 11540 m= 53 mr = 761 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 18809 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) : 0.5588697 object centre at (A) : 40.80700 16.07900 30.42700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5328759E-02 2.0243144E-02 midg,1,midg; midg,igrid,midg -1.3706900E-02 -1.7035216E-03 1,midg,midg; igrid,midg,midg -6.0047943E-04 -1.2457938E-03 gauss-seidel spectral radius is 0.9982448 estimated iterations to convergence 190 setup time was (sec) 0.8000000 now iterating at: 19:33:11 rms-change max change #iterations 3.264409 165.8824 at 10iterations 1.373307 58.77026 at 20iterations 0.5789627 24.74249 at 30iterations 0.2442203 8.980881 at 40iterations 0.1036543 4.157257 at 50iterations 4.3571569E-02 1.851902 at 60iterations 1.8448029E-02 0.7071152 at 70iterations 7.7851657E-03 0.2912619 at 80iterations 3.2991988E-03 0.1238337 at 90iterations 1.3957610E-03 5.1938534E-02 at 100iterations 5.9109717E-04 2.5421143E-02 at 110iterations 2.4985141E-04 8.9745522E-03 at 120iterations finished qdiffx linear iterations at : 19:33:21 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 2.4985141E-04 8.9745522E-03 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 19:33:21 10.279u 0.428s 0:10.99 97.2% 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 Mon Oct 10 2011 at 19:33:21 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: GLM 155 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.514914 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): 17.23000 64.38400 ymin,ymax (A): -9.664001 41.82200 zmin,zma (A): -1.423000 62.27700 x,y,z range (A): 47.15400 51.48600 63.70000 scale (grids/A): 2.514914 object centre (A): 40.80700 16.07900 30.42700 number of atom coordinates read : 2588 total number of charged atoms : 2443 net assigned charge : 1.906022 assigned positive charge : 385.1130 centred at (gu) : 91.09834 86.89235 87.92136 assigned negative charge : -383.2077 centred at (gu) : 90.88816 86.51311 88.21033 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 136295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24706 grid for indexing accessible points = 1.400000 m= 61177 mr = 94711 m= 16914 mr = 47183 m= 2754 mr = 12121 m= 199 mr = 1657 m= 12 mr = 62 m= 0 mr = 1 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 61616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 19518 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) : 1.676609 object centre at (A) : 40.80700 16.07900 30.42700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3514244 0.4911687 midg,1,midg; midg,igrid,midg -0.1491134 -1.4376272E-02 1,midg,midg; igrid,midg,midg -9.3841407E-04 -3.6842816E-02 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.490000 now iterating at: 19:33:23 rms-change max change #iterations 8.392034 283.3897 at 10iterations 4.764999 140.1223 at 20iterations 2.675148 73.26495 at 30iterations 1.492066 33.83183 at 40iterations 0.8323033 19.65969 at 50iterations 0.4625062 11.68172 at 60iterations 0.2561100 6.100010 at 70iterations 0.1419264 3.187832 at 80iterations 7.8233398E-02 1.805636 at 90iterations 4.3260142E-02 0.9321308 at 100iterations 2.3875386E-02 0.5302505 at 110iterations 1.3197047E-02 0.2868261 at 120iterations 7.2684786E-03 0.1517563 at 130iterations 4.0150951E-03 8.5046768E-02 at 140iterations 2.2123477E-03 4.6388626E-02 at 150iterations 1.2184397E-03 2.5405407E-02 at 160iterations 6.7312922E-04 1.4806747E-02 at 170iterations 3.7057258E-04 7.6179504E-03 at 180iterations finished qdiffx linear iterations at : 19:33:39 total time elapsed so far: 17.41000 # loops : 180 mean,max change (kT/e) : 3.7057258E-04 7.6179504E-03 energy calculations done at 17.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.58000 DelPhi exited at 19:33:40 17.587u 0.487s 0:18.62 96.9% 0+0k 0+0io 0pf+0w