Tue Oct 11 03:51:52 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 Tue Oct 11 2011 at 03:51:52 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6401381 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): -9.326000 36.59700 ymin,ymax (A): -26.83000 21.66100 zmin,zma (A): -10.32300 45.29000 x,y,z range (A): 45.92300 48.49100 55.61300 scale (grids/A): 0.6401381 object centre (A): 13.63550 -2.584500 17.48350 number of atom coordinates read : 2761 total number of charged atoms : 2603 net assigned charge : 1.926020 assigned positive charge : 420.2256 centred at (gu) : 89.36797 90.48158 91.89503 assigned negative charge : -418.3002 centred at (gu) : 89.14868 90.34528 91.86076 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 55945 no. pairs analyzed = 55945 no. exposed pairs = 3328 no. arc points = 23070 no. surface atoms = 1127 nbur = 1634 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 4277 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2211 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9029 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2957630E-10 1.0771718E-08 midg,1,midg; midg,igrid,midg -1.3060312E-08 2.1907512E-08 1,midg,midg; igrid,midg,midg -2.9155046E-08 2.5963189E-08 gauss-seidel spectral radius is 0.9873670 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 03:51:52 rms-change max change #iterations 0.1573590 21.75154 at 10iterations 1.5725125E-02 1.999685 at 20iterations 1.6118999E-03 0.2037977 at 30iterations 1.8506791E-04 2.7931213E-02 at 40iterations 2.8555154E-05 4.0130615E-03 at 50iterations finished qdiffx linear iterations at : 03:51:55 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.8555154E-05 4.0130615E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:51:56 3.421u 0.166s 0:04.09 87.5% 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 Tue Oct 11 2011 at 03:51:56 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.920414 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): -9.326000 36.59700 ymin,ymax (A): -26.83000 21.66100 zmin,zma (A): -10.32300 45.29000 x,y,z range (A): 45.92300 48.49100 55.61300 scale (grids/A): 1.920414 object centre (A): 13.63550 -2.584500 17.48350 number of atom coordinates read : 2761 total number of charged atoms : 2603 net assigned charge : 1.926020 assigned positive charge : 420.2256 centred at (gu) : 88.10358 91.44395 95.68455 assigned negative charge : -418.3002 centred at (gu) : 87.44590 91.03548 95.58167 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 29996 mr = 57649 m= 4719 mr = 22565 m= 274 mr = 3037 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 926 time to turn everything in is 0.4000000 number of dielectric boundary points 32985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20492 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) : 0.6401381 object centre at (A) : 13.63550 -2.584500 17.48350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0470101E-02 6.0540508E-04 midg,1,midg; midg,igrid,midg -1.7454654E-02 8.3281631E-03 1,midg,midg; igrid,midg,midg -2.0551614E-02 4.6981711E-02 gauss-seidel spectral radius is 0.9986704 estimated iterations to convergence 217 setup time was (sec) 0.6100000 now iterating at: 03:51:57 rms-change max change #iterations 4.555914 186.9423 at 10iterations 2.159749 77.74579 at 20iterations 1.025975 31.37676 at 30iterations 0.4871037 14.70016 at 40iterations 0.2303567 7.252916 at 50iterations 0.1094190 3.347069 at 60iterations 5.1827177E-02 1.566418 at 70iterations 2.4517423E-02 0.7519684 at 80iterations 1.1622364E-02 0.3582282 at 90iterations 5.5194106E-03 0.1706829 at 100iterations 2.6288342E-03 8.3858490E-02 at 110iterations 1.2525835E-03 4.1532516E-02 at 120iterations finished qdiffx linear iterations at : 03:52:04 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.2525835E-03 4.1532516E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 03:52:04 7.864u 0.207s 0:08.38 96.1% 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 Tue Oct 11 2011 at 03:52:05 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.880621 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): -9.326000 36.59700 ymin,ymax (A): -26.83000 21.66100 zmin,zma (A): -10.32300 45.29000 x,y,z range (A): 45.92300 48.49100 55.61300 scale (grids/A): 2.880621 object centre (A): 13.63550 -2.584500 17.48350 number of atom coordinates read : 2761 total number of charged atoms : 2603 net assigned charge : 1.926020 assigned positive charge : 420.2256 centred at (gu) : 87.15515 92.16582 98.52671 assigned negative charge : -418.3002 centred at (gu) : 86.16872 91.55328 98.37257 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 187904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23070 grid for indexing accessible points = 1.400000 m= 97200 mr = 139220 m= 35564 mr = 80492 m= 8549 mr = 28925 m= 1239 mr = 6511 m= 78 mr = 849 m= 0 mr = 22 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3165 time to turn everything in is 1.040000 number of dielectric boundary points 74515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 20823 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) : 1.920414 object centre at (A) : 13.63550 -2.584500 17.48350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2439964 0.2171694 midg,1,midg; midg,igrid,midg -0.1943507 5.0807964E-02 1,midg,midg; igrid,midg,midg -0.1759799 0.4278111 gauss-seidel spectral radius is 0.9992649 estimated iterations to convergence 291 setup time was (sec) 1.290000 now iterating at: 03:52:06 rms-change max change #iterations 10.53524 464.6755 at 10iterations 6.163908 141.1521 at 20iterations 3.597617 71.25233 at 30iterations 2.089543 38.86736 at 40iterations 1.211734 24.57304 at 50iterations 0.7004771 13.50088 at 60iterations 0.4054039 7.325895 at 70iterations 0.2348667 4.742241 at 80iterations 0.1353708 2.523232 at 90iterations 7.8412160E-02 1.509584 at 100iterations 4.5231931E-02 0.8733177 at 110iterations 2.6167510E-02 0.4722977 at 120iterations 1.5143227E-02 0.2571411 at 130iterations 8.7835053E-03 0.1547914 at 140iterations 5.1064370E-03 9.0431213E-02 at 150iterations 2.9948836E-03 5.3948402E-02 at 160iterations 1.7781819E-03 3.0788422E-02 at 170iterations 1.0723214E-03 1.9332886E-02 at 180iterations finished qdiffx linear iterations at : 03:52:17 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.0723214E-03 1.9332886E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 03:52:18 12.819u 0.204s 0:13.44 96.8% 0+0k 0+0io 0pf+0w