Sun Oct 9 01:47:49 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 Sun Oct 9 2011 at 01:47:49 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIT 88 has a net charge of 0.5140 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: 0.5555035 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): -47.19000 7.226000 ymin,ymax (A): 176.3940 239.7290 zmin,zma (A): 78.97000 143.0560 x,y,z range (A): 54.41600 63.33499 64.08600 scale (grids/A): 0.5555035 object centre (A): -19.98200 208.0615 111.0130 number of atom coordinates read : 3371 total number of charged atoms : 3228 net assigned charge : 15.01403 assigned positive charge : 499.8643 centred at (gu) : 89.77190 89.83670 90.72049 assigned negative charge : -484.8522 centred at (gu) : 89.69025 89.82217 90.89343 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7093 nv = 96 ne = 84 npr = 64538 no. pairs analyzed = 64538 no. exposed pairs = 4659 no. arc points = 32475 no. surface atoms = 1551 nbur = 1820 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 = 1.540000 m= 315 mr = 3505 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2200000 number of dielectric boundary points 3892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3315 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9105 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6117739E-09 -5.5210242E-10 midg,1,midg; midg,igrid,midg 1.2656105E-09 1.4590819E-09 1,midg,midg; igrid,midg,midg 5.4580235E-10 2.0814981E-09 gauss-seidel spectral radius is 0.9833323 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 01:47:49 rms-change max change #iterations 8.6290821E-02 16.97782 at 10iterations 6.0165450E-03 0.9739265 at 20iterations 4.3072627E-04 6.0340881E-02 at 30iterations 3.3651660E-05 4.8561096E-03 at 40iterations 3.6211197E-06 4.3392181E-04 at 50iterations finished qdiffx linear iterations at : 01:47:53 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.6211197E-06 4.3392181E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 01:47:53 3.465u 0.305s 0:04.16 90.3% 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 Sun Oct 9 2011 at 01:47:53 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIT 88 has a net charge of 0.5140 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: 1.666511 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): -47.19000 7.226000 ymin,ymax (A): 176.3940 239.7290 zmin,zma (A): 78.97000 143.0560 x,y,z range (A): 54.41600 63.33499 64.08600 scale (grids/A): 1.666511 object centre (A): -19.98200 208.0615 111.0130 number of atom coordinates read : 3371 total number of charged atoms : 3228 net assigned charge : 15.01403 assigned positive charge : 499.8643 centred at (gu) : 89.31458 89.50925 92.16050 assigned negative charge : -484.8522 centred at (gu) : 89.07034 89.46638 92.68002 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78259 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32475 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25174 mr = 51990 m= 2895 mr = 17117 m= 96 mr = 1452 m= 0 mr = 13 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 884 time to turn everything in is 0.3800000 number of dielectric boundary points 35852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 24847 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) : 0.5555035 object centre at (A) : -19.98200 208.0615 111.0130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2013350E-02 -1.1402168E-02 midg,1,midg; midg,igrid,midg 3.1763684E-02 2.8418811E-02 1,midg,midg; igrid,midg,midg 1.4267592E-03 1.6842432E-02 gauss-seidel spectral radius is 0.9983235 estimated iterations to convergence 194 setup time was (sec) 0.6000000 now iterating at: 01:47:54 rms-change max change #iterations 3.685940 164.3530 at 10iterations 1.582051 73.14059 at 20iterations 0.6788568 23.31726 at 30iterations 0.2913224 10.71241 at 40iterations 0.1261496 4.094725 at 50iterations 5.4222286E-02 1.837697 at 60iterations 2.3342345E-02 0.8518448 at 70iterations 1.0076331E-02 0.3079944 at 80iterations 4.3276921E-03 0.1569023 at 90iterations 1.8738295E-03 6.2004089E-02 at 100iterations 8.0504600E-04 2.8983355E-02 at 110iterations 3.4772989E-04 1.1520386E-02 at 120iterations finished qdiffx linear iterations at : 01:48:01 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 3.4772989E-04 1.1520386E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 01:48:02 7.907u 0.248s 0:08.53 95.4% 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 Sun Oct 9 2011 at 01:48:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIT 88 has a net charge of 0.5140 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: 2.499766 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): -47.19000 7.226000 ymin,ymax (A): 176.3940 239.7290 zmin,zma (A): 78.97000 143.0560 x,y,z range (A): 54.41600 63.33499 64.08600 scale (grids/A): 2.499766 object centre (A): -19.98200 208.0615 111.0130 number of atom coordinates read : 3371 total number of charged atoms : 3228 net assigned charge : 15.01403 assigned positive charge : 499.8643 centred at (gu) : 88.97171 89.26345 93.24053 assigned negative charge : -484.8522 centred at (gu) : 88.60546 89.19947 94.01989 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 181347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32475 grid for indexing accessible points = 1.400000 m= 85436 mr = 127454 m= 26064 mr = 66849 m= 4673 mr = 19465 m= 374 mr = 3101 m= 7 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 3010 time to turn everything in is 1.000000 number of dielectric boundary points 80875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 25795 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) : 1.666511 object centre at (A) : -19.98200 208.0615 111.0130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1923648 -0.1015161 midg,1,midg; midg,igrid,midg 0.3489655 0.4785885 1,midg,midg; igrid,midg,midg -3.1678144E-02 0.1950867 gauss-seidel spectral radius is 0.9992016 estimated iterations to convergence 279 setup time was (sec) 1.260000 now iterating at: 01:48:03 rms-change max change #iterations 9.467088 269.8074 at 10iterations 5.461297 159.9314 at 20iterations 3.126463 72.81927 at 30iterations 1.788679 39.86109 at 40iterations 1.014895 19.97260 at 50iterations 0.5772367 12.11456 at 60iterations 0.3260739 7.685483 at 70iterations 0.1844212 3.700745 at 80iterations 0.1040706 2.291491 at 90iterations 5.8864627E-02 1.145443 at 100iterations 3.3105537E-02 0.6535048 at 110iterations 1.8642720E-02 0.3588296 at 120iterations 1.0477037E-02 0.2138824 at 130iterations 5.9048291E-03 0.1136932 at 140iterations 3.3236623E-03 6.2528610E-02 at 150iterations 1.8602723E-03 3.5842896E-02 at 160iterations 1.0481942E-03 1.9248962E-02 at 170iterations 5.8926677E-04 1.0887146E-02 at 180iterations finished qdiffx linear iterations at : 01:48:15 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 5.8926677E-04 1.0887146E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 01:48:15 13.062u 0.255s 0:13.76 96.7% 0+0k 0+0io 0pf+0w