Sun Oct 9 23:36:16 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 Sun Oct 9 2011 at 23:36:16 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 = 2810 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5352980 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): -40.60500 25.90000 ymin,ymax (A): -26.74800 23.90700 zmin,zma (A): -7.710000 36.48000 x,y,z range (A): 66.50500 50.65500 44.19000 scale (grids/A): 0.5352980 object centre (A): -7.352502 -1.420500 14.38500 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.89069 89.77854 89.47813 assigned negative charge : -423.6726 centred at (gu) : 89.95274 89.86782 89.43410 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5139 nv = 96 ne = 84 npr = 54468 no. pairs analyzed = 54468 no. exposed pairs = 3758 no. arc points = 27896 no. surface atoms = 1256 nbur = 1554 mkacc time = 0.1100000 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 = 1.596000 m= 203 mr = 2376 m= 1 mr = 6 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 0.2800000 number of dielectric boundary points 2961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2824 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7785629E-11 3.4066894E-10 midg,1,midg; midg,igrid,midg 6.0874022E-10 -1.6701536E-10 1,midg,midg; igrid,midg,midg 4.7592147E-10 -5.8321716E-11 gauss-seidel spectral radius is 0.9820092 estimated iterations to convergence 61 setup time was (sec) 0.5100000 now iterating at: 23:36:17 rms-change max change #iterations 6.4287432E-02 12.55567 at 10iterations 3.9587272E-03 0.8395691 at 20iterations 2.4714594E-04 4.6524048E-02 at 30iterations 1.5748303E-05 2.9506683E-03 at 40iterations 1.0562510E-06 2.3269653E-04 at 50iterations finished qdiffx linear iterations at : 23:36:20 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.0562510E-06 2.3269653E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 23:36:20 3.290u 0.219s 0:03.80 92.1% 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 Sun Oct 9 2011 at 23:36:20 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 = 2810 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.605894 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): -40.60500 25.90000 ymin,ymax (A): -26.74800 23.90700 zmin,zma (A): -7.710000 36.48000 x,y,z range (A): 66.50500 50.65500 44.19000 scale (grids/A): 1.605894 object centre (A): -7.352502 -1.420500 14.38500 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.67167 89.33480 88.43377 assigned negative charge : -423.6726 centred at (gu) : 89.85806 89.60328 88.30225 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 56986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15545 mr = 35912 m= 1339 mr = 10039 m= 23 mr = 535 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 893 time to turn everything in is 0.3900000 number of dielectric boundary points 27407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20292 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) : 0.5352980 object centre at (A) : -7.352502 -1.420500 14.38500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3966367E-03 3.7734691E-04 midg,1,midg; midg,igrid,midg 7.6751979E-03 2.0417026E-03 1,midg,midg; igrid,midg,midg 1.3988242E-02 2.2163463E-03 gauss-seidel spectral radius is 0.9981036 estimated iterations to convergence 182 setup time was (sec) 0.6600000 now iterating at: 23:36:21 rms-change max change #iterations 3.064656 162.9031 at 10iterations 1.241868 70.78846 at 20iterations 0.5054560 22.32352 at 30iterations 0.2064764 7.668550 at 40iterations 8.4154859E-02 3.326849 at 50iterations 3.4240808E-02 1.324234 at 60iterations 1.3984762E-02 0.5814743 at 70iterations 5.6829993E-03 0.2295370 at 80iterations 2.3248349E-03 9.4584942E-02 at 90iterations 9.4687368E-04 3.6911011E-02 at 100iterations 3.8780528E-04 1.7856598E-02 at 110iterations 1.5789509E-04 6.7319870E-03 at 120iterations finished qdiffx linear iterations at : 23:36:27 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 1.5789509E-04 6.7319870E-03 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 23:36:28 7.179u 0.253s 0:07.85 94.5% 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 Sun Oct 9 2011 at 23:36:28 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 = 2810 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.408841 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): -40.60500 25.90000 ymin,ymax (A): -26.74800 23.90700 zmin,zma (A): -7.710000 36.48000 x,y,z range (A): 66.50500 50.65500 44.19000 scale (grids/A): 2.408841 object centre (A): -7.352502 -1.420500 14.38500 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.50713 89.00210 87.65060 assigned negative charge : -423.6726 centred at (gu) : 89.78719 89.40501 87.45338 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 132635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55165 mr = 88937 m= 14045 mr = 41895 m= 1983 mr = 10083 m= 81 mr = 1143 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2905 time to turn everything in is 0.9300000 number of dielectric boundary points 61834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 21304 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) : 1.605894 object centre at (A) : -7.352502 -1.420500 14.38500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2433105E-02 4.7910181E-03 midg,1,midg; midg,igrid,midg 0.1186527 6.9861509E-02 1,midg,midg; igrid,midg,midg 9.7627148E-02 1.3079012E-02 gauss-seidel spectral radius is 0.9991074 estimated iterations to convergence 264 setup time was (sec) 1.230000 now iterating at: 23:36:30 rms-change max change #iterations 7.998552 277.5141 at 10iterations 4.357191 124.3052 at 20iterations 2.377781 54.93377 at 30iterations 1.295470 28.84542 at 40iterations 0.7021389 16.43335 at 50iterations 0.3815061 8.627064 at 60iterations 0.2067666 4.895051 at 70iterations 0.1118632 2.386721 at 80iterations 6.0804725E-02 1.261101 at 90iterations 3.2965567E-02 0.7468194 at 100iterations 1.7841728E-02 0.4443030 at 110iterations 9.6853720E-03 0.2210426 at 120iterations 5.2421200E-03 0.1163445 at 130iterations 2.8362635E-03 6.0781479E-02 at 140iterations 1.5433127E-03 3.3546448E-02 at 150iterations 8.3492312E-04 1.7090797E-02 at 160iterations 4.5311070E-04 1.0009766E-02 at 170iterations 2.4567355E-04 5.4063797E-03 at 180iterations finished qdiffx linear iterations at : 23:36:40 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 2.4567355E-04 5.4063797E-03 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 23:36:40 11.460u 0.246s 0:11.98 97.6% 0+0k 0+0io 0pf+0w