Mon Oct 10 19:34:00 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 19:34:00 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3944 !!! WARNING: HIR 255 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5834057 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): -71.29700 -10.27600 ymin,ymax (A): -27.60700 24.23600 zmin,zma (A): -36.48600 24.13100 x,y,z range (A): 61.02100 51.84300 60.61700 scale (grids/A): 0.5834057 object centre (A): -40.78650 -1.685500 -6.177500 number of atom coordinates read : 3944 total number of charged atoms : 3868 net assigned charge : 5.014020 assigned positive charge : 614.3371 centred at (gu) : 90.73509 91.19320 88.92165 assigned negative charge : -609.3261 centred at (gu) : 90.64942 91.19785 89.01438 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9108 nv = 96 ne = 84 npr = 76373 no. pairs analyzed = 76373 no. exposed pairs = 5169 no. arc points = 35002 no. surface atoms = 1727 nbur = 2217 mkacc time = 0.2600000 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 = 1.484000 m= 431 mr = 4928 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.5400000 number of dielectric boundary points 4574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3675 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 11670 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4896172E-09 -1.5275344E-09 midg,1,midg; midg,igrid,midg 1.0157115E-09 1.3262035E-09 1,midg,midg; igrid,midg,midg -1.4556482E-09 4.7844373E-09 gauss-seidel spectral radius is 0.9849157 estimated iterations to convergence 67 setup time was (sec) 0.9100000 now iterating at: 19:34:02 rms-change max change #iterations 0.1180439 15.50905 at 10iterations 9.7688632E-03 1.301908 at 20iterations 9.9462061E-04 0.1283722 at 30iterations 2.1746749E-04 3.0466080E-02 at 40iterations 7.8461388E-05 1.2100220E-02 at 50iterations finished qdiffx linear iterations at : 19:34:06 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 7.8461388E-05 1.2100220E-02 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 19:34:07 5.246u 0.428s 0:06.39 88.5% 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 19:34:07 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3944 !!! WARNING: HIR 255 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.750217 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): -71.29700 -10.27600 ymin,ymax (A): -27.60700 24.23600 zmin,zma (A): -36.48600 24.13100 x,y,z range (A): 61.02100 51.84300 60.61700 scale (grids/A): 1.750217 object centre (A): -40.78650 -1.685500 -6.177500 number of atom coordinates read : 3944 total number of charged atoms : 3868 net assigned charge : 5.014020 assigned positive charge : 614.3371 centred at (gu) : 92.20398 93.57813 86.76383 assigned negative charge : -609.3261 centred at (gu) : 91.94794 93.59325 87.04293 start vw surface at 0.1900000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 99695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35002 grid for indexing accessible points = 1.400000 m= 35660 mr = 70080 m= 4744 mr = 25228 m= 224 mr = 2491 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1118 time to turn everything in is 1.000000 number of dielectric boundary points 42462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 30098 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) : 0.5834057 object centre at (A) : -40.78650 -1.685500 -6.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6619917E-03 -1.3632699E-02 midg,1,midg; midg,igrid,midg 7.1285232E-03 1.9882312E-02 1,midg,midg; igrid,midg,midg -4.3880190E-03 3.0292492E-02 gauss-seidel spectral radius is 0.9985240 estimated iterations to convergence 206 setup time was (sec) 1.350000 now iterating at: 19:34:09 rms-change max change #iterations 4.669278 183.4561 at 10iterations 2.116037 76.35553 at 20iterations 0.9624686 28.30309 at 30iterations 0.4379904 14.24780 at 40iterations 0.1998460 5.995800 at 50iterations 9.0720080E-02 2.649410 at 60iterations 4.1231379E-02 1.254004 at 70iterations 1.8797727E-02 0.5555055 at 80iterations 8.5944664E-03 0.2868423 at 90iterations 3.9148363E-03 0.1160958 at 100iterations 1.7968849E-03 5.0645828E-02 at 110iterations 8.3429221E-04 2.6111603E-02 at 120iterations finished qdiffx linear iterations at : 19:34:19 total time elapsed so far: 11.79000 # loops : 120 mean,max change (kT/e) : 8.3429221E-04 2.6111603E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 19:34:20 12.035u 0.498s 0:13.15 95.2% 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 19:34:20 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3944 !!! WARNING: HIR 255 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.625325 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): -71.29700 -10.27600 ymin,ymax (A): -27.60700 24.23600 zmin,zma (A): -36.48600 24.13100 x,y,z range (A): 61.02100 51.84300 60.61700 scale (grids/A): 2.625325 object centre (A): -40.78650 -1.685500 -6.177500 number of atom coordinates read : 3944 total number of charged atoms : 3868 net assigned charge : 5.014020 assigned positive charge : 614.3371 centred at (gu) : 93.30576 95.36683 85.14555 assigned negative charge : -609.3261 centred at (gu) : 92.92189 95.38970 85.56418 start vw surface at 0.2000000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 231354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35002 grid for indexing accessible points = 1.400000 m= 117388 mr = 170528 m= 39277 mr = 94505 m= 7894 mr = 30085 m= 895 mr = 5421 m= 34 mr = 495 m= 0 mr = 3 time to grow re-entrant surface = 1.650000 no. cavity mid-points inaccessible to solvent = 3629 time to turn everything in is 2.620000 number of dielectric boundary points 95805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.810000 number of grid points assigned charge 30934 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) : 1.750217 object centre at (A) : -40.78650 -1.685500 -6.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4987839 -0.1435403 midg,1,midg; midg,igrid,midg 0.1672003 0.2568911 1,midg,midg; igrid,midg,midg 0.1421196 0.3820686 gauss-seidel spectral radius is 0.9992633 estimated iterations to convergence 291 setup time was (sec) 3.030000 now iterating at: 19:34:23 rms-change max change #iterations 11.58176 278.4661 at 10iterations 6.911385 169.4202 at 20iterations 4.068446 79.35144 at 30iterations 2.384387 45.12742 at 40iterations 1.394007 26.57318 at 50iterations 0.8127429 13.88031 at 60iterations 0.4728209 8.538080 at 70iterations 0.2743887 4.680346 at 80iterations 0.1590487 2.732664 at 90iterations 9.2022493E-02 1.661072 at 100iterations 5.3248659E-02 0.9455719 at 110iterations 3.0795248E-02 0.5408213 at 120iterations 1.7821517E-02 0.2952747 at 130iterations 1.0341289E-02 0.1699948 at 140iterations 6.0186903E-03 0.1049271 at 150iterations 3.5502014E-03 7.0432663E-02 at 160iterations 2.1447893E-03 4.1259766E-02 at 170iterations 1.3501409E-03 2.7896881E-02 at 180iterations finished qdiffx linear iterations at : 19:34:42 total time elapsed so far: 21.16000 # loops : 180 mean,max change (kT/e) : 1.3501409E-03 2.7896881E-02 energy calculations done at 21.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.38000 DelPhi exited at 19:34:42 21.387u 0.500s 0:22.30 98.1% 0+0k 0+0io 0pf+0w