Mon Oct 10 18:52:23 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+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 Mon Oct 10 2011 at 18:52:23 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 = 2480 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: 0.6114107 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): 40.09600 92.56000 ymin,ymax (A): -69.70900 -11.48300 zmin,zma (A): 68.36900 111.4150 x,y,z range (A): 52.46400 58.22600 43.04601 scale (grids/A): 0.6114107 object centre (A): 66.32800 -40.59600 89.89200 number of atom coordinates read : 2480 total number of charged atoms : 2341 net assigned charge : 0.5000106 assigned positive charge : 372.8948 centred at (gu) : 90.65434 92.17461 90.57763 assigned negative charge : -372.3955 centred at (gu) : 90.70541 92.17910 90.73289 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6286 nv = 96 ne = 84 npr = 49701 no. pairs analyzed = 49701 no. exposed pairs = 3356 no. arc points = 22574 no. surface atoms = 1119 nbur = 1361 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3390 m= 2 mr = 25 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 0.3000000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2250 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9288713E-09 -8.4350278E-09 midg,1,midg; midg,igrid,midg 3.7806178E-10 2.6057859E-10 1,midg,midg; igrid,midg,midg 2.4902636E-09 -2.4883753E-09 gauss-seidel spectral radius is 0.9861414 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 18:52:24 rms-change max change #iterations 0.1143547 18.60996 at 10iterations 1.0398128E-02 1.490250 at 20iterations 1.2079860E-03 0.1752892 at 30iterations 2.5848855E-04 3.8990021E-02 at 40iterations 7.6044242E-05 1.1210918E-02 at 50iterations finished qdiffx linear iterations at : 18:52:28 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 7.6044242E-05 1.1210918E-02 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 18:52:28 4.694u 0.385s 0:05.48 92.5% 0+0k 0+0io 5pf+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 18:52:28 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 = 2480 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: 1.834232 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): 40.09600 92.56000 ymin,ymax (A): -69.70900 -11.48300 zmin,zma (A): 68.36900 111.4150 x,y,z range (A): 52.46400 58.22600 43.04601 scale (grids/A): 1.834232 object centre (A): 66.32800 -40.59600 89.89200 number of atom coordinates read : 2480 total number of charged atoms : 2341 net assigned charge : 0.5000106 assigned positive charge : 372.8948 centred at (gu) : 91.96236 96.52347 91.73216 assigned negative charge : -372.3955 centred at (gu) : 92.11606 96.53703 92.19846 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 24854 mr = 46823 m= 3697 mr = 17992 m= 180 mr = 2050 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 29699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 18303 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) : 0.6114107 object centre at (A) : 66.32800 -40.59600 89.89200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2403248E-02 -1.1853316E-02 midg,1,midg; midg,igrid,midg 2.2309778E-02 -1.5296306E-02 1,midg,midg; igrid,midg,midg 2.8303811E-02 -1.8518219E-02 gauss-seidel spectral radius is 0.9985211 estimated iterations to convergence 206 setup time was (sec) 0.8800000 now iterating at: 18:52:30 rms-change max change #iterations 3.849206 176.3159 at 10iterations 1.748273 65.90639 at 20iterations 0.7935140 29.69515 at 30iterations 0.3611189 13.38204 at 40iterations 0.1643638 5.826558 at 50iterations 7.4393265E-02 2.646757 at 60iterations 3.4017731E-02 1.144413 at 70iterations 1.5402744E-02 0.5079842 at 80iterations 7.0924927E-03 0.2551422 at 90iterations 3.2724598E-03 0.1209450 at 100iterations 1.5501945E-03 5.5330276E-02 at 110iterations 7.6367456E-04 2.7973175E-02 at 120iterations finished qdiffx linear iterations at : 18:52:40 total time elapsed so far: 11.42000 # loops : 120 mean,max change (kT/e) : 7.6367456E-04 2.7973175E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 18:52:41 11.586u 0.427s 0:12.28 97.7% 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 18:52:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 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: 2.751348 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): 40.09600 92.56000 ymin,ymax (A): -69.70900 -11.48300 zmin,zma (A): 68.36900 111.4150 x,y,z range (A): 52.46400 58.22600 43.04601 scale (grids/A): 2.751348 object centre (A): 66.32800 -40.59600 89.89200 number of atom coordinates read : 2480 total number of charged atoms : 2341 net assigned charge : 0.5000106 assigned positive charge : 372.8948 centred at (gu) : 92.94339 99.78513 92.59806 assigned negative charge : -372.3955 centred at (gu) : 93.17397 99.80541 93.29754 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 157196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 80322 mr = 114195 m= 28796 mr = 64834 m= 6289 mr = 22556 m= 767 mr = 4423 m= 41 mr = 428 m= 0 mr = 15 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 66960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18725 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) : 1.834232 object centre at (A) : 66.32800 -40.59600 89.89200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1697214 -9.8791935E-02 midg,1,midg; midg,igrid,midg 0.5614629 -0.2143363 1,midg,midg; igrid,midg,midg 0.4560332 -0.3460878 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.830000 now iterating at: 18:52:43 rms-change max change #iterations 9.400620 291.6211 at 10iterations 5.554409 143.9577 at 20iterations 3.243478 72.54347 at 30iterations 1.882631 40.87215 at 40iterations 1.087616 27.96540 at 50iterations 0.6257871 13.18664 at 60iterations 0.3592373 7.905122 at 70iterations 0.2058072 4.304647 at 80iterations 0.1175917 2.389900 at 90iterations 6.7277208E-02 1.309122 at 100iterations 3.8405407E-02 0.7711067 at 110iterations 2.1895684E-02 0.4192528 at 120iterations 1.2552740E-02 0.2416039 at 130iterations 7.1895118E-03 0.1378078 at 140iterations 4.1315989E-03 8.1575394E-02 at 150iterations 2.4080339E-03 4.4071198E-02 at 160iterations 1.4311176E-03 3.0986786E-02 at 170iterations 8.7733392E-04 1.8044472E-02 at 180iterations finished qdiffx linear iterations at : 18:53:00 total time elapsed so far: 19.04000 # loops : 180 mean,max change (kT/e) : 8.7733392E-04 1.8044472E-02 energy calculations done at 19.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.22000 DelPhi exited at 18:53:01 19.224u 0.443s 0:20.06 98.0% 0+0k 0+0io 0pf+0w