Sat Oct 8 14:08:29 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 Sat Oct 8 2011 at 14:08:29 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 = 2980 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6395975 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 0.6395975 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.514007 assigned positive charge : 448.2376 centred at (gu) : 88.75707 89.58425 91.75306 assigned negative charge : -446.7244 centred at (gu) : 88.69331 89.45312 91.73906 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8107 nv = 96 ne = 84 npr = 62541 no. pairs analyzed = 62541 no. exposed pairs = 3307 no. arc points = 23205 no. surface atoms = 1127 nbur = 1853 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4752 m= 0 mr = 50 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2280 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6788017E-10 6.1053758E-09 midg,1,midg; midg,igrid,midg -1.6690864E-08 1.7749448E-08 1,midg,midg; igrid,midg,midg -8.1099296E-09 8.2042870E-09 gauss-seidel spectral radius is 0.9873621 estimated iterations to convergence 73 setup time was (sec) 0.6900000 now iterating at: 14:08:30 rms-change max change #iterations 0.1550033 22.58209 at 10iterations 1.5709464E-02 2.462666 at 20iterations 1.6582736E-03 0.2028675 at 30iterations 2.0277684E-04 2.7641296E-02 at 40iterations 3.0108135E-05 4.7626495E-03 at 50iterations finished qdiffx linear iterations at : 14:08:35 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 3.0108135E-05 4.7626495E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 14:08:35 5.204u 0.448s 0:05.92 95.2% 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 8 2011 at 14:08:35 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 = 2980 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.918792 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 1.918792 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.514007 assigned positive charge : 448.2376 centred at (gu) : 86.27052 88.75220 95.25860 assigned negative charge : -446.7244 centred at (gu) : 86.07956 88.35908 95.21698 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 31928 mr = 64151 m= 4804 mr = 24239 m= 296 mr = 3021 m= 3 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1180 time to turn everything in is 0.7100000 number of dielectric boundary points 33768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22324 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) : 0.6395975 object centre at (A) : 15.55400 -0.1040001 19.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1577939E-02 1.3810180E-02 midg,1,midg; midg,igrid,midg -4.7435737E-03 2.4632206E-02 1,midg,midg; igrid,midg,midg -3.1153899E-02 1.9002020E-02 gauss-seidel spectral radius is 0.9986818 estimated iterations to convergence 218 setup time was (sec) 1.060000 now iterating at: 14:08:37 rms-change max change #iterations 4.685604 215.7088 at 10iterations 2.236812 67.08479 at 20iterations 1.058740 30.16238 at 30iterations 0.5056998 14.74070 at 40iterations 0.2394390 7.526693 at 50iterations 0.1139178 3.301306 at 60iterations 5.4331850E-02 1.589822 at 70iterations 2.5800111E-02 0.7375317 at 80iterations 1.2275766E-02 0.3324175 at 90iterations 5.8369851E-03 0.1835785 at 100iterations 2.7768083E-03 8.7643623E-02 at 110iterations 1.3257571E-03 3.9690018E-02 at 120iterations finished qdiffx linear iterations at : 14:08:49 total time elapsed so far: 13.03000 # loops : 120 mean,max change (kT/e) : 1.3257571E-03 3.9690018E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 14:08:49 13.198u 0.529s 0:13.99 97.9% 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 8 2011 at 14:08:49 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 = 2980 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.878189 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 2.878189 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.514007 assigned positive charge : 448.2376 centred at (gu) : 84.40572 88.12806 97.88782 assigned negative charge : -446.7244 centred at (gu) : 84.11929 87.53859 97.82558 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 204676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 104839 mr = 154751 m= 36771 mr = 88030 m= 8511 mr = 29926 m= 1253 mr = 6304 m= 83 mr = 864 m= 0 mr = 35 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 3842 time to turn everything in is 1.900000 number of dielectric boundary points 76223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 22676 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) : 1.918792 object centre at (A) : 15.55400 -0.1040001 19.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7165862E-02 0.3029993 midg,1,midg; midg,igrid,midg -4.3355618E-02 0.2761617 1,midg,midg; igrid,midg,midg -0.5200664 0.2377150 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 2.300000 now iterating at: 14:08:52 rms-change max change #iterations 10.84555 336.3814 at 10iterations 6.336909 155.2730 at 20iterations 3.677146 67.15941 at 30iterations 2.135765 44.82284 at 40iterations 1.237306 20.58259 at 50iterations 0.7166924 13.87805 at 60iterations 0.4141218 7.215765 at 70iterations 0.2397147 4.237471 at 80iterations 0.1384481 2.247533 at 90iterations 8.0146752E-02 1.329919 at 100iterations 4.6306171E-02 0.7860413 at 110iterations 2.6783705E-02 0.4479904 at 120iterations 1.5482458E-02 0.2620397 at 130iterations 8.9705521E-03 0.1711826 at 140iterations 5.1719937E-03 9.1234207E-02 at 150iterations 3.0011248E-03 5.0086975E-02 at 160iterations 1.7416442E-03 3.0761719E-02 at 170iterations 1.0125862E-03 1.6740799E-02 at 180iterations finished qdiffx linear iterations at : 14:09:11 total time elapsed so far: 21.27000 # loops : 180 mean,max change (kT/e) : 1.0125862E-03 1.6740799E-02 energy calculations done at 21.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.44000 DelPhi exited at 14:09:12 21.446u 0.547s 0:22.28 98.6% 0+0k 0+0io 0pf+0w