Tue Oct 11 07:52:53 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 07:52:54 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6375472 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 0.6375472 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2246 net assigned charge : 6.961007 assigned positive charge : 363.2404 centred at (gu) : 88.71177 90.29906 89.73417 assigned negative charge : -356.2798 centred at (gu) : 88.72793 90.23408 89.49046 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6640 nv = 96 ne = 84 npr = 47670 no. pairs analyzed = 47670 no. exposed pairs = 2953 no. arc points = 20833 no. surface atoms = 1002 nbur = 1391 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3676 m= 3 mr = 50 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 0.2700000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2041 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6505618E-08 3.1370746E-08 midg,1,midg; midg,igrid,midg 2.7914921E-09 1.6986846E-08 1,midg,midg; igrid,midg,midg 1.4564236E-08 6.0573280E-09 gauss-seidel spectral radius is 0.9872362 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 07:52:54 rms-change max change #iterations 0.1440880 20.92975 at 10iterations 1.4057852E-02 2.017449 at 20iterations 1.6018599E-03 0.2477417 at 30iterations 2.1859526E-04 3.4439087E-02 at 40iterations 4.0932435E-05 6.0033798E-03 at 50iterations finished qdiffx linear iterations at : 07:52:58 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 4.0932435E-05 6.0033798E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 07:52:59 4.461u 0.395s 0:05.34 90.8% 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 Tue Oct 11 2011 at 07:52:59 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 1.912642 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 1.912642 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2246 net assigned charge : 6.961007 assigned positive charge : 363.2404 centred at (gu) : 86.13487 90.89684 89.20216 assigned negative charge : -356.2798 centred at (gu) : 86.18375 90.70215 88.47119 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20833 grid for indexing accessible points = 1.400000 m= 26712 mr = 49287 m= 4130 mr = 19967 m= 230 mr = 2544 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17645 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) : 0.6375472 object centre at (A) : 26.11650 0.1545000 32.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0591153E-02 4.8065424E-02 midg,1,midg; midg,igrid,midg -1.0869001E-03 4.3243403E-03 1,midg,midg; igrid,midg,midg 2.1505482E-02 2.7659087E-02 gauss-seidel spectral radius is 0.9986281 estimated iterations to convergence 214 setup time was (sec) 0.8400000 now iterating at: 07:53:00 rms-change max change #iterations 4.119623 177.3115 at 10iterations 1.921740 67.71773 at 20iterations 0.9056230 32.36639 at 30iterations 0.4229320 13.56863 at 40iterations 0.1988704 6.554726 at 50iterations 9.2834413E-02 2.992165 at 60iterations 4.3687824E-02 1.529644 at 70iterations 2.0479364E-02 0.7119389 at 80iterations 9.6283155E-03 0.2825851 at 90iterations 4.5473622E-03 0.1499233 at 100iterations 2.1545361E-03 7.0082664E-02 at 110iterations 1.0345625E-03 3.5390854E-02 at 120iterations finished qdiffx linear iterations at : 07:53:10 total time elapsed so far: 10.21000 # loops : 120 mean,max change (kT/e) : 1.0345625E-03 3.5390854E-02 energy calculations done at 10.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 07:53:10 10.378u 0.463s 0:11.33 95.5% 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 07:53:10 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: LEV 97 has a net charge of 0.0020 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.868962 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 2.868962 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2246 net assigned charge : 6.961007 assigned positive charge : 363.2404 centred at (gu) : 84.20218 91.34518 88.80310 assigned negative charge : -356.2798 centred at (gu) : 84.27561 91.05310 87.70672 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 163252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20833 grid for indexing accessible points = 1.400000 m= 85699 mr = 118951 m= 31656 mr = 70975 m= 7171 mr = 25551 m= 967 mr = 5273 m= 55 mr = 660 m= 0 mr = 27 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 67363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 17964 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) : 1.912642 object centre at (A) : 26.11650 0.1545000 32.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2850375 0.4841730 midg,1,midg; midg,igrid,midg -1.2946407E-02 -6.4053260E-02 1,midg,midg; igrid,midg,midg 0.1052498 0.1849862 gauss-seidel spectral radius is 0.9992507 estimated iterations to convergence 288 setup time was (sec) 1.840000 now iterating at: 07:53:13 rms-change max change #iterations 9.650168 383.7209 at 10iterations 5.630250 127.6460 at 20iterations 3.265374 69.64568 at 30iterations 1.885247 43.78947 at 40iterations 1.090742 23.27498 at 50iterations 0.6271371 13.47692 at 60iterations 0.3614393 7.534248 at 70iterations 0.2075135 3.616571 at 80iterations 0.1191217 2.305281 at 90iterations 6.8347946E-02 1.206631 at 100iterations 3.9228637E-02 0.7348255 at 110iterations 2.2513935E-02 0.4301568 at 120iterations 1.2877495E-02 0.2681427 at 130iterations 7.3937597E-03 0.1498985 at 140iterations 4.2520999E-03 8.5735321E-02 at 150iterations 2.4494871E-03 4.5269012E-02 at 160iterations 1.4137815E-03 2.8034210E-02 at 170iterations 8.2026760E-04 1.6042709E-02 at 180iterations finished qdiffx linear iterations at : 07:53:28 total time elapsed so far: 17.50000 # loops : 180 mean,max change (kT/e) : 8.2026760E-04 1.6042709E-02 energy calculations done at 17.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.67000 DelPhi exited at 07:53:29 17.672u 0.466s 0:18.59 97.5% 0+0k 0+0io 0pf+0w