Sun Oct 9 17:26:32 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 Sun Oct 9 2011 at 17:26:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5632555 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 0.5632555 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.621040 assigned positive charge : 755.6410 centred at (gu) : 88.32330 89.22316 89.10638 assigned negative charge : -754.0255 centred at (gu) : 88.21111 89.24162 89.07711 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 10283 nv = 96 ne = 84 npr = 99087 no. pairs analyzed = 99087 no. exposed pairs = 5911 no. arc points = 39722 no. surface atoms = 2015 nbur = 2908 mkacc time = 0.1700000 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 = 1.540000 m= 525 mr = 5920 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4016 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13419 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6924675E-10 6.8820877E-10 midg,1,midg; midg,igrid,midg 7.5817802E-10 -1.1969195E-10 1,midg,midg; igrid,midg,midg -3.2530167E-09 1.7099627E-09 gauss-seidel spectral radius is 0.9838837 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 17:26:33 rms-change max change #iterations 0.1158603 15.49995 at 10iterations 1.0752360E-02 1.436478 at 20iterations 2.8311401E-03 0.3226929 at 30iterations 1.3053780E-03 0.1404800 at 40iterations 6.3295913E-04 7.2834492E-02 at 50iterations finished qdiffx linear iterations at : 17:26:36 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.3295913E-04 7.2834492E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:26:36 3.486u 0.171s 0:03.93 92.8% 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 Sun Oct 9 2011 at 17:26:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.689767 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 1.689767 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.621040 assigned positive charge : 755.6410 centred at (gu) : 84.96828 87.66816 87.31790 assigned negative charge : -754.0255 centred at (gu) : 84.63325 87.72478 87.23112 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 114490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39722 grid for indexing accessible points = 1.400000 m= 40824 mr = 82960 m= 5226 mr = 29566 m= 192 mr = 2866 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 45313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 36912 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) : 0.5632555 object centre at (A) : 33.84050 22.42000 30.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4426956E-02 -2.7438734E-02 midg,1,midg; midg,igrid,midg 1.8112954E-02 1.0312354E-02 1,midg,midg; igrid,midg,midg -1.6999282E-02 3.9926499E-02 gauss-seidel spectral radius is 0.9984881 estimated iterations to convergence 204 setup time was (sec) 0.7600000 now iterating at: 17:26:37 rms-change max change #iterations 4.919574 222.6503 at 10iterations 2.207480 84.91010 at 20iterations 0.9937904 30.06977 at 30iterations 0.4489399 13.32748 at 40iterations 0.2025673 5.407700 at 50iterations 9.2003092E-02 2.441574 at 60iterations 4.1986529E-02 1.054840 at 70iterations 1.9597217E-02 0.5499268 at 80iterations 9.6543636E-03 0.2775574 at 90iterations 5.3101480E-03 0.1552963 at 100iterations 3.3500241E-03 9.0866089E-02 at 110iterations 2.3791401E-03 5.6404114E-02 at 120iterations finished qdiffx linear iterations at : 17:26:44 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 2.3791401E-03 5.6404114E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 17:26:45 8.002u 0.207s 0:08.52 96.2% 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 Sun Oct 9 2011 at 17:26:45 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4923 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.534650 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): 3.226000 64.45500 ymin,ymax (A): -8.618999 53.45900 zmin,zma (A): -1.215000 61.98900 x,y,z range (A): 61.22900 62.07800 63.20400 scale (grids/A): 2.534650 object centre (A): 33.84050 22.42000 30.38700 number of atom coordinates read : 4923 total number of charged atoms : 4783 net assigned charge : 1.621040 assigned positive charge : 755.6410 centred at (gu) : 82.45198 86.50193 85.97643 assigned negative charge : -754.0255 centred at (gu) : 81.94979 86.58715 85.84665 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 265623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39722 grid for indexing accessible points = 1.400000 m= 136337 mr = 201309 m= 44653 mr = 111283 m= 8579 mr = 34850 m= 761 mr = 5888 m= 22 mr = 401 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 102242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 38240 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) : 1.689767 object centre at (A) : 33.84050 22.42000 30.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4316159 -0.6960595 midg,1,midg; midg,igrid,midg -1.0141657E-02 1.1828436E-03 1,midg,midg; igrid,midg,midg -0.3489703 0.6129904 gauss-seidel spectral radius is 0.9992677 estimated iterations to convergence 292 setup time was (sec) 1.640000 now iterating at: 17:26:47 rms-change max change #iterations 12.39747 309.4722 at 10iterations 7.362698 165.1542 at 20iterations 4.347796 93.59226 at 30iterations 2.553400 46.11737 at 40iterations 1.496462 25.09509 at 50iterations 0.8731983 15.17283 at 60iterations 0.5080698 8.701878 at 70iterations 0.2956755 5.084524 at 80iterations 0.1720014 2.896706 at 90iterations 9.9729754E-02 1.614353 at 100iterations 5.7994973E-02 0.9951134 at 110iterations 3.3819564E-02 0.5169830 at 120iterations 1.9927083E-02 0.3284416 at 130iterations 1.1956338E-02 0.1982193 at 140iterations 7.4310750E-03 0.1225567 at 150iterations 4.8818761E-03 8.5342407E-02 at 160iterations 3.4477068E-03 5.8845520E-02 at 170iterations 2.6241511E-03 3.7940979E-02 at 180iterations finished qdiffx linear iterations at : 17:26:59 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 2.6241511E-03 3.7940979E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 17:26:59 13.760u 0.215s 0:14.31 97.6% 0+0k 0+0io 0pf+0w