Mon Oct 10 18:53:01 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 18:53:01 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 245 has a net charge of 0.5140 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 : 0.5280104 assigned positive charge : 376.9787 centred at (gu) : 90.65720 92.13292 90.63309 assigned negative charge : -376.4515 centred at (gu) : 90.70954 92.13417 90.78268 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 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 0.2900000 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 6.6933725E-09 -8.2853733E-09 midg,1,midg; midg,igrid,midg 2.9398398E-10 5.4533694E-10 1,midg,midg; igrid,midg,midg 2.5812110E-09 -2.5773830E-09 gauss-seidel spectral radius is 0.9861414 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 18:53:02 rms-change max change #iterations 0.1165746 18.86700 at 10iterations 1.0610257E-02 1.547110 at 20iterations 1.2530873E-03 0.1881409 at 30iterations 2.7385011E-04 4.0971756E-02 at 40iterations 8.0891761E-05 1.1948109E-02 at 50iterations finished qdiffx linear iterations at : 18:53:06 total time elapsed so far: 4.750000 # loops : 50 mean,max change (kT/e) : 8.0891761E-05 1.1948109E-02 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 18:53:07 4.917u 0.389s 0:05.63 93.9% 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 18:53:07 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 245 has a net charge of 0.5140 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: 1.834232 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 : 0.5280104 assigned positive charge : 376.9787 centred at (gu) : 91.97093 96.39828 91.89849 assigned negative charge : -376.4515 centred at (gu) : 92.12847 96.40218 92.34783 start vw surface at 0.1200000 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 0.5800000 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 0.7000000 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 1.2307982E-02 -1.0959956E-02 midg,1,midg; midg,igrid,midg 2.1332420E-02 -1.5145207E-02 1,midg,midg; igrid,midg,midg 2.8473999E-02 -1.8555868E-02 gauss-seidel spectral radius is 0.9985211 estimated iterations to convergence 206 setup time was (sec) 0.8800000 now iterating at: 18:53:08 rms-change max change #iterations 3.897985 176.3161 at 10iterations 1.771020 65.90639 at 20iterations 0.8036042 30.74282 at 30iterations 0.3657308 14.21088 at 40iterations 0.1664939 5.821404 at 50iterations 7.5352192E-02 2.758358 at 60iterations 3.4461424E-02 1.173363 at 70iterations 1.5612317E-02 0.5157127 at 80iterations 7.1963957E-03 0.2598381 at 90iterations 3.3311846E-03 0.1240158 at 100iterations 1.5849565E-03 5.6612015E-02 at 110iterations 7.8739662E-04 2.9483795E-02 at 120iterations finished qdiffx linear iterations at : 18:53:18 total time elapsed so far: 11.25000 # loops : 120 mean,max change (kT/e) : 7.8739662E-04 2.9483795E-02 energy calculations done at 11.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 18:53:19 11.422u 0.417s 0:12.21 96.8% 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 18:53:19 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 245 has a net charge of 0.5140 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 : 0.5280104 assigned positive charge : 376.9787 centred at (gu) : 92.95622 99.59734 92.84756 assigned negative charge : -376.4515 centred at (gu) : 93.19258 99.60313 93.52157 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 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 = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 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 1.650000 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 0.1687566 -8.9816444E-02 midg,1,midg; midg,igrid,midg 0.5498527 -0.2127245 1,midg,midg; igrid,midg,midg 0.4579411 -0.3462404 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.840000 now iterating at: 18:53:21 rms-change max change #iterations 9.509127 291.6212 at 10iterations 5.613268 143.9793 at 20iterations 3.276891 72.63950 at 30iterations 1.901208 40.80790 at 40iterations 1.097668 27.91527 at 50iterations 0.6314804 13.03546 at 60iterations 0.3624242 7.964011 at 70iterations 0.2076053 4.296185 at 80iterations 0.1185942 2.392990 at 90iterations 6.7824408E-02 1.281685 at 100iterations 3.8718496E-02 0.7783928 at 110iterations 2.2081424E-02 0.4267147 at 120iterations 1.2659357E-02 0.2398148 at 130iterations 7.2549372E-03 0.1387901 at 140iterations 4.1744127E-03 8.4120750E-02 at 150iterations 2.4374300E-03 4.3733597E-02 at 160iterations 1.4544491E-03 3.0707359E-02 at 170iterations 8.9673669E-04 1.8730102E-02 at 180iterations finished qdiffx linear iterations at : 18:53:39 total time elapsed so far: 19.12000 # loops : 180 mean,max change (kT/e) : 8.9673669E-04 1.8730102E-02 energy calculations done at 19.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.30000 DelPhi exited at 18:53:39 19.307u 0.461s 0:20.13 98.1% 0+0k 0+0io 0pf+0w