Tue Oct 11 07:57:57 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 07:57:57 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 57 has a net charge of 0.5140 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLU 245 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5949695 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 0.5949695 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2350 net assigned charge : 5.781008 assigned positive charge : 382.1152 centred at (gu) : 89.48737 90.09555 89.80782 assigned negative charge : -376.3347 centred at (gu) : 89.52213 90.06190 89.66092 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5677 nv = 96 ne = 84 npr = 50525 no. pairs analyzed = 50525 no. exposed pairs = 2916 no. arc points = 20375 no. surface atoms = 998 nbur = 1492 mkacc time = 9.0000004E-02 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 = 1.456000 m= 245 mr = 3124 m= 2 mr = 18 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 0.1800000 number of dielectric boundary points 2782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5303883E-09 6.1965810E-09 midg,1,midg; midg,igrid,midg 1.0628843E-09 3.1884848E-09 1,midg,midg; igrid,midg,midg 3.5409642E-09 9.4399599E-10 gauss-seidel spectral radius is 0.9853671 estimated iterations to convergence 68 setup time was (sec) 0.3600000 now iterating at: 07:57:57 rms-change max change #iterations 0.1045946 22.78468 at 10iterations 9.0888133E-03 1.337847 at 20iterations 7.9003803E-04 0.1378078 at 30iterations 7.4291042E-05 1.2611389E-02 at 40iterations 7.6072106E-06 1.1634827E-03 at 50iterations finished qdiffx linear iterations at : 07:58:00 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.6072106E-06 1.1634827E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 07:58:01 3.332u 0.185s 0:03.93 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 Tue Oct 11 2011 at 07:58:01 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 57 has a net charge of 0.5140 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLU 245 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.784908 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 1.784908 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2350 net assigned charge : 5.781008 assigned positive charge : 382.1152 centred at (gu) : 88.46177 90.28645 89.42327 assigned negative charge : -376.3347 centred at (gu) : 88.56645 90.18555 88.98266 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 20787 mr = 43203 m= 2577 mr = 15101 m= 115 mr = 1476 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 972 time to turn everything in is 0.3000000 number of dielectric boundary points 25812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18280 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) : 0.5949695 object centre at (A) : 23.54850 0.2065001 31.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1529630E-02 2.5999378E-02 midg,1,midg; midg,igrid,midg -1.8980958E-03 3.3909075E-03 1,midg,midg; igrid,midg,midg 3.1739574E-02 2.5459059E-02 gauss-seidel spectral radius is 0.9984300 estimated iterations to convergence 200 setup time was (sec) 0.5200000 now iterating at: 07:58:01 rms-change max change #iterations 3.646540 175.1414 at 10iterations 1.619779 62.48206 at 20iterations 0.7192495 26.15120 at 30iterations 0.3182851 12.25951 at 40iterations 0.1416368 5.122382 at 50iterations 6.2732175E-02 2.512875 at 60iterations 2.7965233E-02 1.215126 at 70iterations 1.2424618E-02 0.4185486 at 80iterations 5.5171289E-03 0.1830597 at 90iterations 2.4473907E-03 8.4383965E-02 at 100iterations 1.0903311E-03 3.8869321E-02 at 110iterations 4.8493742E-04 1.7299652E-02 at 120iterations finished qdiffx linear iterations at : 07:58:08 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 4.8493742E-04 1.7299652E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 07:58:09 7.579u 0.202s 0:08.06 96.4% 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 07:58:09 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 57 has a net charge of 0.5140 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLU 245 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.677363 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 2.677363 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2350 net assigned charge : 5.781008 assigned positive charge : 382.1152 centred at (gu) : 87.69247 90.42953 89.13478 assigned negative charge : -376.3347 centred at (gu) : 87.84961 90.27819 88.47401 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 69938 mr = 104554 m= 22200 mr = 57269 m= 4435 mr = 17465 m= 552 mr = 3135 m= 12 mr = 352 m= 0 mr = 2 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 3363 time to turn everything in is 0.7600000 number of dielectric boundary points 58317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18793 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) : 1.784908 object centre at (A) : 23.54850 0.2065001 31.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1604109 0.3377211 midg,1,midg; midg,igrid,midg -2.3821453E-02 -1.5981872E-02 1,midg,midg; igrid,midg,midg 0.3003821 0.2491634 gauss-seidel spectral radius is 0.9991916 estimated iterations to convergence 278 setup time was (sec) 0.9900000 now iterating at: 07:58:10 rms-change max change #iterations 8.746391 287.8259 at 10iterations 4.966875 121.9025 at 20iterations 2.800357 62.55814 at 30iterations 1.571797 35.18015 at 40iterations 0.8842403 19.51772 at 50iterations 0.4951536 10.93893 at 60iterations 0.2772637 6.064054 at 70iterations 0.1551296 3.271694 at 80iterations 8.7449126E-02 1.774774 at 90iterations 4.8816461E-02 1.042657 at 100iterations 2.7371963E-02 0.5687237 at 110iterations 1.5289989E-02 0.3030930 at 120iterations 8.5860305E-03 0.1710320 at 130iterations 4.8084483E-03 9.6881866E-02 at 140iterations 2.7009102E-03 5.4769516E-02 at 150iterations 1.5133310E-03 3.0057907E-02 at 160iterations 8.4935554E-04 1.7166138E-02 at 170iterations 4.7955054E-04 1.1531830E-02 at 180iterations finished qdiffx linear iterations at : 07:58:21 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 4.7955054E-04 1.1531830E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 07:58:21 12.016u 0.197s 0:12.49 97.6% 0+0k 0+0io 0pf+0w