Sat Oct 15 13:41:22 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 Sat Oct 15 2011 at 13:41:22 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 106 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6822014 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): -18.18800 33.99600 ymin,ymax (A): -25.62400 21.22800 zmin,zma (A): -5.286000 43.17500 x,y,z range (A): 52.18400 46.85200 48.46100 scale (grids/A): 0.6822014 object centre (A): 7.904001 -2.198000 18.94450 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -7.099974 assigned positive charge : 324.7238 centred at (gu) : 87.99813 91.43327 87.29189 assigned negative charge : -331.8239 centred at (gu) : 88.27290 91.51032 87.25314 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6736 nv = 96 ne = 84 npr = 44194 no. pairs analyzed = 44194 no. exposed pairs = 2747 no. arc points = 19419 no. surface atoms = 918 nbur = 1230 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3647 m= 6 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.1800000 number of dielectric boundary points 3441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5880472E-08 -1.3069963E-08 midg,1,midg; midg,igrid,midg -8.3665341E-09 -7.3704882E-08 1,midg,midg; igrid,midg,midg 6.8617219E-08 -7.6659596E-08 gauss-seidel spectral radius is 0.9888185 estimated iterations to convergence 77 setup time was (sec) 0.3900000 now iterating at: 13:41:23 rms-change max change #iterations 0.1794354 28.65727 at 10iterations 2.0242780E-02 2.830246 at 20iterations 2.3257362E-03 0.3417664 at 30iterations 2.5900052E-04 3.9151192E-02 at 40iterations 2.9586583E-05 4.2572021E-03 at 50iterations finished qdiffx linear iterations at : 13:41:30 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 2.9586583E-05 4.2572021E-03 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 13:41:31 3.800u 0.212s 0:08.87 45.2% 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 Sat Oct 15 2011 at 13:41:31 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 106 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.046604 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): -18.18800 33.99600 ymin,ymax (A): -25.62400 21.22800 zmin,zma (A): -5.286000 43.17500 x,y,z range (A): 52.18400 46.85200 48.46100 scale (grids/A): 2.046604 object centre (A): 7.904001 -2.198000 18.94450 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -7.099974 assigned positive charge : 324.7238 centred at (gu) : 83.99452 94.29971 81.87563 assigned negative charge : -331.8239 centred at (gu) : 84.81867 94.53106 81.75938 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19419 grid for indexing accessible points = 1.400000 m= 26577 mr = 48283 m= 4530 mr = 19679 m= 300 mr = 2857 m= 5 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3863 time to turn everything in is 0.3500000 number of dielectric boundary points 31757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15878 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) : 0.6822014 object centre at (A) : 7.904001 -2.198000 18.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9164795E-02 4.4805600E-04 midg,1,midg; midg,igrid,midg 4.6704221E-03 -1.8576438E-02 1,midg,midg; igrid,midg,midg 1.2927220E-02 -7.8592032E-02 gauss-seidel spectral radius is 0.9987596 estimated iterations to convergence 225 setup time was (sec) 0.5700000 now iterating at: 13:41:32 rms-change max change #iterations 4.417926 188.5732 at 10iterations 2.129029 78.05968 at 20iterations 1.033084 35.16445 at 30iterations 0.5016414 15.26325 at 40iterations 0.2429067 7.136177 at 50iterations 0.1180023 3.927368 at 60iterations 5.7000481E-02 1.714419 at 70iterations 2.7576825E-02 0.8403449 at 80iterations 1.3358079E-02 0.4502926 at 90iterations 6.4925528E-03 0.2067297 at 100iterations 3.1450391E-03 9.4463348E-02 at 110iterations 1.5283249E-03 5.1721811E-02 at 120iterations finished qdiffx linear iterations at : 13:41:45 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.5283249E-03 5.1721811E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 13:41:46 8.024u 0.198s 0:14.76 55.6% 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 Sat Oct 15 2011 at 13:41:46 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: ASL 106 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.069906 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): -18.18800 33.99600 ymin,ymax (A): -25.62400 21.22800 zmin,zma (A): -5.286000 43.17500 x,y,z range (A): 52.18400 46.85200 48.46100 scale (grids/A): 3.069906 object centre (A): 7.904001 -2.198000 18.94450 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -7.099974 assigned positive charge : 324.7238 centred at (gu) : 80.99165 96.44939 77.81348 assigned negative charge : -331.8239 centred at (gu) : 82.22813 96.79653 77.63911 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 164070 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19419 grid for indexing accessible points = 1.400000 m= 83998 mr = 116796 m= 32344 mr = 68577 m= 8491 mr = 26153 m= 1437 mr = 6440 m= 100 mr = 965 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 12934 time to turn everything in is 1.000000 number of dielectric boundary points 71453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 16055 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) : 2.046604 object centre at (A) : 7.904001 -2.198000 18.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1101564 2.1176539E-02 midg,1,midg; midg,igrid,midg -7.0957504E-03 -9.6596599E-02 1,midg,midg; igrid,midg,midg 0.4151513 -0.8056382 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 13:41:51 rms-change max change #iterations 10.18821 363.8702 at 10iterations 5.978684 133.0170 at 20iterations 3.485053 81.71843 at 30iterations 2.029847 40.20472 at 40iterations 1.181785 22.14960 at 50iterations 0.6892069 12.46254 at 60iterations 0.4001069 7.191811 at 70iterations 0.2323713 4.044849 at 80iterations 0.1351459 2.445200 at 90iterations 7.8356668E-02 1.453373 at 100iterations 4.5487825E-02 0.8710709 at 110iterations 2.6353667E-02 0.4638214 at 120iterations 1.5307858E-02 0.3283081 at 130iterations 8.8911029E-03 0.1571388 at 140iterations 5.1558069E-03 9.4028473E-02 at 150iterations 2.9976096E-03 4.9971581E-02 at 160iterations 1.7359958E-03 3.3168793E-02 at 170iterations 1.0091696E-03 1.7823696E-02 at 180iterations finished qdiffx linear iterations at : 13:42:11 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 1.0091696E-03 1.7823696E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 13:42:12 14.009u 0.315s 0:25.42 56.2% 0+0k 0+0io 0pf+0w