Sat Oct 15 11:59:51 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 11:59:51 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 = 2490 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5891600 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 0.5891600 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.500032 assigned positive charge : 361.0822 centred at (gu) : 89.79306 89.69566 89.58195 assigned negative charge : -351.5829 centred at (gu) : 89.81255 89.79111 89.64713 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5765 nv = 96 ne = 84 npr = 49841 no. pairs analyzed = 49841 no. exposed pairs = 3322 no. arc points = 23954 no. surface atoms = 1111 nbur = 1379 mkacc time = 0.1400000 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 = 1.484000 m= 263 mr = 2859 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2900000 number of dielectric boundary points 3150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7344 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7825277E-09 1.1771742E-09 midg,1,midg; midg,igrid,midg 5.4093694E-09 5.3085097E-10 1,midg,midg; igrid,midg,midg 3.4413439E-09 2.2631641E-09 gauss-seidel spectral radius is 0.9850940 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 11:59:52 rms-change max change #iterations 9.3377516E-02 15.04436 at 10iterations 7.5678667E-03 1.276196 at 20iterations 6.2440976E-04 9.5817566E-02 at 30iterations 6.0099512E-05 9.7236633E-03 at 40iterations 8.5101628E-06 1.6193390E-03 at 50iterations finished qdiffx linear iterations at : 11:59:56 total time elapsed so far: 5.040000 # loops : 50 mean,max change (kT/e) : 8.5101628E-06 1.6193390E-03 energy calculations done at 5.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.210000 DelPhi exited at 11:59:57 5.217u 0.499s 0:06.12 93.1% 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 Sat Oct 15 2011 at 11:59:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.767480 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 1.767480 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.500032 assigned positive charge : 361.0822 centred at (gu) : 89.37877 89.08652 88.74519 assigned negative charge : -351.5829 centred at (gu) : 89.43746 89.37329 88.94135 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 20224 mr = 41068 m= 2774 mr = 13691 m= 122 mr = 1525 m= 0 mr = 26 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.5300000 number of dielectric boundary points 29418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18332 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) : 0.5891600 object centre at (A) : 72.31950 59.48950 13.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8559489E-02 1.3744554E-02 midg,1,midg; midg,igrid,midg 1.5807260E-02 -4.9650171E-03 1,midg,midg; igrid,midg,midg 1.8315703E-02 3.5054535E-02 gauss-seidel spectral radius is 0.9984185 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 11:59:58 rms-change max change #iterations 3.435937 175.9213 at 10iterations 1.513170 58.75254 at 20iterations 0.6656566 24.12312 at 30iterations 0.2945381 10.78525 at 40iterations 0.1301534 4.410984 at 50iterations 5.7132605E-02 2.304687 at 60iterations 2.5277805E-02 0.8968353 at 70iterations 1.1157493E-02 0.3631897 at 80iterations 4.9288305E-03 0.1718187 at 90iterations 2.1749246E-03 7.8156531E-02 at 100iterations 9.6411421E-04 3.8748741E-02 at 110iterations 4.2661899E-04 1.4892578E-02 at 120iterations finished qdiffx linear iterations at : 12:00:09 total time elapsed so far: 12.05000 # loops : 120 mean,max change (kT/e) : 4.2661899E-04 1.4892578E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 12:00:10 12.236u 0.543s 0:13.22 96.5% 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 Sat Oct 15 2011 at 12:00:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.651220 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 2.651220 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.500032 assigned positive charge : 361.0822 centred at (gu) : 89.06811 88.62966 88.11777 assigned negative charge : -351.5829 centred at (gu) : 89.15617 89.05994 88.41196 start vw surface at 0.1000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 145100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 67057 mr = 100582 m= 21891 mr = 52311 m= 4638 mr = 16507 m= 547 mr = 3192 m= 19 mr = 327 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 1962 time to turn everything in is 1.350000 number of dielectric boundary points 66333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 18820 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) : 1.767480 object centre at (A) : 72.31950 59.48950 13.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3226605 0.1791075 midg,1,midg; midg,igrid,midg 0.1945039 -8.6024925E-02 1,midg,midg; igrid,midg,midg 0.3957537 0.5511551 gauss-seidel spectral radius is 0.9992065 estimated iterations to convergence 280 setup time was (sec) 1.720000 now iterating at: 12:00:12 rms-change max change #iterations 8.614023 316.3048 at 10iterations 4.996205 154.7774 at 20iterations 2.867808 67.03041 at 30iterations 1.636326 43.00505 at 40iterations 0.9308105 21.84049 at 50iterations 0.5289217 11.80960 at 60iterations 0.2997857 6.348486 at 70iterations 0.1693628 4.015263 at 80iterations 9.5742509E-02 1.934814 at 90iterations 5.4024674E-02 1.143543 at 100iterations 3.0596077E-02 0.5956416 at 110iterations 1.7238051E-02 0.3656197 at 120iterations 9.7311251E-03 0.2065544 at 130iterations 5.4878076E-03 0.1073399 at 140iterations 3.0896021E-03 6.7303836E-02 at 150iterations 1.7366356E-03 3.4618378E-02 at 160iterations 9.7909220E-04 1.8859863E-02 at 170iterations 5.5190345E-04 1.1543274E-02 at 180iterations finished qdiffx linear iterations at : 12:00:33 total time elapsed so far: 22.71000 # loops : 180 mean,max change (kT/e) : 5.5190345E-04 1.1543274E-02 energy calculations done at 22.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.89000 DelPhi exited at 12:00:34 22.894u 0.568s 0:23.78 98.6% 0+0k 0+0io 0pf+0w