Sat Oct 15 11:32:50 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 Sat Oct 15 2011 at 11:32:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 0.6473551 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): 6.974000 61.96700 ymin,ymax (A): 75.21500 122.5780 zmin,zma (A): -8.237000 33.40900 x,y,z range (A): 54.99300 47.36299 41.64600 scale (grids/A): 0.6473551 object centre (A): 34.47050 98.89650 12.58600 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.000003 assigned positive charge : 298.5528 centred at (gu) : 87.33570 90.83044 91.03886 assigned negative charge : -295.5529 centred at (gu) : 87.43464 90.76159 90.97066 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5605 nv = 96 ne = 84 npr = 41021 no. pairs analyzed = 41021 no. exposed pairs = 2548 no. arc points = 17894 no. surface atoms = 858 nbur = 1152 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2990 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1710 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9507580E-09 1.5127114E-08 midg,1,midg; midg,igrid,midg -2.1095825E-09 1.4551808E-08 1,midg,midg; igrid,midg,midg 2.7294291E-08 -3.2312328E-09 gauss-seidel spectral radius is 0.9875822 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 11:32:51 rms-change max change #iterations 0.1328159 26.28595 at 10iterations 1.3390845E-02 2.207352 at 20iterations 1.3676713E-03 0.2330170 at 30iterations 1.3862480E-04 2.1132469E-02 at 40iterations 1.4635530E-05 2.1438599E-03 at 50iterations finished qdiffx linear iterations at : 11:32:55 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 1.4635530E-05 2.1438599E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.330000 DelPhi exited at 11:32:56 5.339u 0.476s 0:06.24 92.9% 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 Sat Oct 15 2011 at 11:32:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 1.942065 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): 6.974000 61.96700 ymin,ymax (A): 75.21500 122.5780 zmin,zma (A): -8.237000 33.40900 x,y,z range (A): 54.99300 47.36299 41.64600 scale (grids/A): 1.942065 object centre (A): 34.47050 98.89650 12.58600 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.000003 assigned positive charge : 298.5528 centred at (gu) : 82.00700 92.49113 93.11679 assigned negative charge : -295.5529 centred at (gu) : 82.30405 92.28465 92.91197 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 60782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17894 grid for indexing accessible points = 1.400000 m= 21169 mr = 41570 m= 3372 mr = 15249 m= 236 mr = 2087 m= 3 mr = 76 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 0.5100000 number of dielectric boundary points 26580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14763 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) : 0.6473551 object centre at (A) : 34.47050 98.89650 12.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1224244E-04 2.1896297E-02 midg,1,midg; midg,igrid,midg 1.8036127E-03 3.3335906E-02 1,midg,midg; igrid,midg,midg -3.1792540E-02 -3.3924885E-02 gauss-seidel spectral radius is 0.9986196 estimated iterations to convergence 213 setup time was (sec) 0.8500000 now iterating at: 11:32:57 rms-change max change #iterations 3.792423 203.0545 at 10iterations 1.759083 63.40276 at 20iterations 0.8234558 26.95365 at 30iterations 0.3833613 13.66980 at 40iterations 0.1788660 6.210621 at 50iterations 8.3309159E-02 3.059723 at 60iterations 3.8966771E-02 1.425983 at 70iterations 1.8210240E-02 0.6735115 at 80iterations 8.4597981E-03 0.3162079 at 90iterations 3.9602942E-03 0.1417150 at 100iterations 1.8509693E-03 6.5592766E-02 at 110iterations 8.6264679E-04 2.9844284E-02 at 120iterations finished qdiffx linear iterations at : 11:33:09 total time elapsed so far: 12.06000 # loops : 120 mean,max change (kT/e) : 8.6264679E-04 2.9844284E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 11:33:09 12.235u 0.544s 0:13.21 96.6% 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 Sat Oct 15 2011 at 11:33:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 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: 2.913098 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): 6.974000 61.96700 ymin,ymax (A): 75.21500 122.5780 zmin,zma (A): -8.237000 33.40900 x,y,z range (A): 54.99300 47.36299 41.64600 scale (grids/A): 2.913098 object centre (A): 34.47050 98.89650 12.58600 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.000003 assigned positive charge : 298.5528 centred at (gu) : 78.01048 93.73675 94.67516 assigned negative charge : -295.5529 centred at (gu) : 78.45604 93.42698 94.36800 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 140562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17894 grid for indexing accessible points = 1.400000 m= 68938 mr = 100923 m= 24334 mr = 55672 m= 6098 mr = 19179 m= 998 mr = 4515 m= 38 mr = 674 m= 0 mr = 14 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 59991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 15008 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) : 1.942065 object centre at (A) : 34.47050 98.89650 12.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1987670E-02 0.2377691 midg,1,midg; midg,igrid,midg -3.3015545E-02 0.3310974 1,midg,midg; igrid,midg,midg -0.5415682 -0.5078959 gauss-seidel spectral radius is 0.9992431 estimated iterations to convergence 287 setup time was (sec) 1.760000 now iterating at: 11:33:12 rms-change max change #iterations 8.914626 427.6838 at 10iterations 5.223054 161.9652 at 20iterations 3.021165 68.63345 at 30iterations 1.758256 52.94080 at 40iterations 1.012742 21.12252 at 50iterations 0.5843722 13.32592 at 60iterations 0.3350735 6.844657 at 70iterations 0.1921117 4.198931 at 80iterations 0.1105855 2.406250 at 90iterations 6.3274279E-02 1.264401 at 100iterations 3.6210351E-02 0.7193422 at 110iterations 2.0716062E-02 0.4025240 at 120iterations 1.1854826E-02 0.2436447 at 130iterations 6.7919516E-03 0.1290388 at 140iterations 3.8793553E-03 7.3482513E-02 at 150iterations 2.2263434E-03 4.5044422E-02 at 160iterations 1.2750755E-03 2.5173187E-02 at 170iterations 7.3347718E-04 1.5291214E-02 at 180iterations finished qdiffx linear iterations at : 11:33:30 total time elapsed so far: 20.58000 # loops : 180 mean,max change (kT/e) : 7.3347718E-04 1.5291214E-02 energy calculations done at 20.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.75000 DelPhi exited at 11:33:31 20.755u 0.553s 0:21.58 98.7% 0+0k 0+0io 0pf+0w