Mon Oct 10 11:01:06 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 11:01:06 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: ADP 1586 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5288333 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 0.5288333 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.500037 assigned positive charge : 848.1632 centred at (gu) : 90.89745 88.81570 88.85804 assigned negative charge : -839.6709 centred at (gu) : 90.89234 88.80427 88.91402 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9605 nv = 96 ne = 84 npr = 105876 no. pairs analyzed = 105876 no. exposed pairs = 6506 no. arc points = 43552 no. surface atoms = 2182 nbur = 3167 mkacc time = 0.2300000 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 = 1.624000 m= 386 mr = 5315 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4800000 number of dielectric boundary points 4659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4407 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 12791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2794765E-10 -7.4898643E-11 midg,1,midg; midg,igrid,midg 2.4814176E-10 2.4837260E-10 1,midg,midg; igrid,midg,midg 1.8207449E-10 3.6612194E-10 gauss-seidel spectral radius is 0.9817455 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 11:01:07 rms-change max change #iterations 8.6536571E-02 12.78839 at 10iterations 5.6245211E-03 0.7492142 at 20iterations 7.1885029E-04 9.4165802E-02 at 30iterations 3.3316953E-04 4.7137380E-02 at 40iterations 1.8115697E-04 2.5221586E-02 at 50iterations finished qdiffx linear iterations at : 11:01:09 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.8115697E-04 2.5221586E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 11:01:10 3.283u 0.179s 0:03.86 89.3% 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 11:01:10 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: ADP 1586 has a net charge of -2.0000 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: 1.586500 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 1.586500 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.500037 assigned positive charge : 848.1632 centred at (gu) : 92.69048 86.44539 86.57254 assigned negative charge : -839.6709 centred at (gu) : 92.67702 86.41299 86.74234 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 109485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34491 mr = 78425 m= 3172 mr = 24041 m= 74 mr = 1410 m= 0 mr = 15 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.7000000 number of dielectric boundary points 43331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 545 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 39428 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) : 0.5288333 object centre at (A) : 13.36900 3.546001 13.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7230333E-03 -4.2418875E-02 midg,1,midg; midg,igrid,midg 4.0920246E-03 2.9524749E-03 1,midg,midg; igrid,midg,midg 2.9142253E-02 1.6157391E-02 gauss-seidel spectral radius is 0.9982951 estimated iterations to convergence 192 setup time was (sec) 0.9800000 now iterating at: 11:01:11 rms-change max change #iterations 4.470279 171.0588 at 10iterations 1.916123 63.38278 at 20iterations 0.8212447 23.07779 at 30iterations 0.3519483 9.768556 at 40iterations 0.1513347 4.168316 at 50iterations 6.4954586E-02 1.918831 at 60iterations 2.7937641E-02 0.7907810 at 70iterations 1.2110753E-02 0.3447189 at 80iterations 5.2748481E-03 0.1614838 at 90iterations 2.4033522E-03 7.2917461E-02 at 100iterations 1.1975253E-03 3.7758827E-02 at 110iterations 7.1936974E-04 2.5017738E-02 at 120iterations finished qdiffx linear iterations at : 11:01:19 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 7.1936974E-04 2.5017738E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.730000 DelPhi exited at 11:01:20 8.728u 0.323s 0:09.45 95.6% 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 Mon Oct 10 2011 at 11:01:20 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: ADP 1586 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.379750 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): -20.29000 47.02800 ymin,ymax (A): -28.30500 35.39700 zmin,zma (A): -19.84500 46.01900 x,y,z range (A): 67.31800 63.70200 65.86400 scale (grids/A): 2.379750 object centre (A): 13.36900 3.546001 13.08700 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 8.500037 assigned positive charge : 848.1632 centred at (gu) : 94.03525 84.66769 84.85827 assigned negative charge : -839.6709 centred at (gu) : 94.01564 84.61955 85.11346 start vw surface at 0.2500000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 254725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43552 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121503 mr = 191168 m= 32682 mr = 97447 m= 4778 mr = 24384 m= 308 mr = 2911 m= 1 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1114 time to turn everything in is 1.800000 number of dielectric boundary points 97940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 41475 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) : 1.586500 object centre at (A) : 13.36900 3.546001 13.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9754141E-03 -1.103745 midg,1,midg; midg,igrid,midg -4.9108531E-02 4.9744472E-02 1,midg,midg; igrid,midg,midg 0.6055319 0.2373032 gauss-seidel spectral radius is 0.9992183 estimated iterations to convergence 282 setup time was (sec) 2.150000 now iterating at: 11:01:22 rms-change max change #iterations 11.84906 312.5152 at 10iterations 6.922729 150.8208 at 20iterations 4.019413 86.20316 at 30iterations 2.315331 47.41411 at 40iterations 1.331986 27.11433 at 50iterations 0.7634937 15.50967 at 60iterations 0.4360261 9.690688 at 70iterations 0.2489173 4.144411 at 80iterations 0.1417852 2.603760 at 90iterations 8.0586143E-02 1.487595 at 100iterations 4.5832913E-02 0.8817492 at 110iterations 2.6058637E-02 0.5061340 at 120iterations 1.4802762E-02 0.2641106 at 130iterations 8.4021315E-03 0.1293106 at 140iterations 4.7821617E-03 8.5307121E-02 at 150iterations 2.7193751E-03 5.2358627E-02 at 160iterations 1.5563067E-03 2.7990222E-02 at 170iterations 9.0151263E-04 1.5644073E-02 at 180iterations finished qdiffx linear iterations at : 11:01:32 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 9.0151263E-04 1.5644073E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 11:01:32 12.315u 0.219s 0:12.86 97.3% 0+0k 0+0io 0pf+0w