Mon Oct 10 09:44:01 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+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 09:44:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6030423 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 0.6030423 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.000013 assigned positive charge : 425.2718 centred at (gu) : 89.04640 88.20701 88.02910 assigned negative charge : -418.2723 centred at (gu) : 89.19679 88.04237 87.93414 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7232 nv = 96 ne = 84 npr = 55702 no. pairs analyzed = 55702 no. exposed pairs = 4456 no. arc points = 32325 no. surface atoms = 1477 nbur = 1435 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3190 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3069 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1487303E-09 4.8210751E-09 midg,1,midg; midg,igrid,midg -5.7528342E-09 6.9369523E-09 1,midg,midg; igrid,midg,midg 1.2141552E-08 -2.4497981E-09 gauss-seidel spectral radius is 0.9858164 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 09:44:01 rms-change max change #iterations 0.1128598 18.97892 at 10iterations 9.2690187E-03 1.417858 at 20iterations 8.3272456E-04 0.1318779 at 30iterations 7.6738783E-05 1.2312889E-02 at 40iterations 1.0814755E-05 1.4686584E-03 at 50iterations finished qdiffx linear iterations at : 09:44:04 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0814755E-05 1.4686584E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 09:44:04 3.416u 0.133s 0:03.84 92.1% 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 09:44:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2912 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.809127 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 1.809127 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.000013 assigned positive charge : 425.2718 centred at (gu) : 87.13852 84.62038 84.08653 assigned negative charge : -418.2723 centred at (gu) : 87.59016 84.12674 83.80225 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 76978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 25314 mr = 46911 m= 3769 mr = 16400 m= 183 mr = 1851 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 41048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21531 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) : 0.6030423 object centre at (A) : 8.082500 -30.50100 28.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3852929E-02 4.4917190E-03 midg,1,midg; midg,igrid,midg 2.6986163E-02 4.1439727E-02 1,midg,midg; igrid,midg,midg 1.4283481E-02 8.9954967E-03 gauss-seidel spectral radius is 0.9985489 estimated iterations to convergence 208 setup time was (sec) 0.9100000 now iterating at: 09:44:06 rms-change max change #iterations 4.014389 182.9022 at 10iterations 1.833845 67.52483 at 20iterations 0.8393045 28.47534 at 30iterations 0.3826795 14.58918 at 40iterations 0.1743180 5.726382 at 50iterations 7.9495341E-02 2.528011 at 60iterations 3.6498100E-02 1.229918 at 70iterations 1.6597329E-02 0.5445557 at 80iterations 7.6204701E-03 0.2626362 at 90iterations 3.4698432E-03 0.1088943 at 100iterations 1.5914316E-03 5.5282593E-02 at 110iterations 7.2628714E-04 2.2073746E-02 at 120iterations finished qdiffx linear iterations at : 09:44:12 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 7.2628714E-04 2.2073746E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 09:44:13 7.861u 0.219s 0:08.59 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 09:44:13 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 = 2912 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.713690 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): -17.85000 34.01500 ymin,ymax (A): -60.01800 -0.9840001 zmin,zma (A): -0.5770000 57.92300 x,y,z range (A): 51.86500 59.03400 58.50000 scale (grids/A): 2.713690 object centre (A): 8.082500 -30.50100 28.67300 number of atom coordinates read : 2912 total number of charged atoms : 2759 net assigned charge : 7.000013 assigned positive charge : 425.2718 centred at (gu) : 85.70770 81.93044 81.12972 assigned negative charge : -418.2723 centred at (gu) : 86.38519 81.19002 80.70334 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 177690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32325 grid for indexing accessible points = 1.400000 m= 81510 mr = 115952 m= 28264 mr = 61194 m= 6368 mr = 20584 m= 771 mr = 4093 m= 49 mr = 396 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 92428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 22069 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) : 1.809127 object centre at (A) : 8.082500 -30.50100 28.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1060591 4.4590883E-02 midg,1,midg; midg,igrid,midg 0.4859471 0.5108097 1,midg,midg; igrid,midg,midg 4.3859746E-02 0.1258705 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 1.860000 now iterating at: 09:44:15 rms-change max change #iterations 10.06353 392.8629 at 10iterations 6.101403 180.6205 at 20iterations 3.639734 104.7507 at 30iterations 2.157684 50.80135 at 40iterations 1.269090 28.68422 at 50iterations 0.7459609 16.25206 at 60iterations 0.4359854 9.446595 at 70iterations 0.2539539 5.685677 at 80iterations 0.1482034 3.578247 at 90iterations 8.6034149E-02 1.826714 at 100iterations 5.0010480E-02 1.111504 at 110iterations 2.8976198E-02 0.5661793 at 120iterations 1.6823461E-02 0.3222638 at 130iterations 9.7368993E-03 0.1885290 at 140iterations 5.6362231E-03 0.1198063 at 150iterations 3.2629829E-03 5.8265209E-02 at 160iterations 1.8877974E-03 4.0514752E-02 at 170iterations 1.0919269E-03 2.0580292E-02 at 180iterations finished qdiffx linear iterations at : 09:44:28 total time elapsed so far: 14.74000 # loops : 180 mean,max change (kT/e) : 1.0919269E-03 2.0580292E-02 energy calculations done at 14.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.95000 DelPhi exited at 09:44:29 14.947u 0.198s 0:15.44 97.9% 0+0k 0+0io 0pf+0w