Sat Oct 8 18:30:47 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 8 2011 at 18:30:47 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6235440 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 0.6235440 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.39689 89.22736 89.97214 assigned negative charge : -387.4045 centred at (gu) : 88.29218 89.26897 89.86095 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6568 nv = 96 ne = 84 npr = 53839 no. pairs analyzed = 53839 no. exposed pairs = 2941 no. arc points = 21178 no. surface atoms = 988 nbur = 1593 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3732 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.3700000 number of dielectric boundary points 3105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5755519E-09 1.1669943E-08 midg,1,midg; midg,igrid,midg 7.9678255E-09 5.6449689E-10 1,midg,midg; igrid,midg,midg -5.9308287E-09 7.9589269E-09 gauss-seidel spectral radius is 0.9866727 estimated iterations to convergence 71 setup time was (sec) 0.6600000 now iterating at: 18:30:48 rms-change max change #iterations 0.1323515 22.74993 at 10iterations 1.2236396E-02 1.905087 at 20iterations 1.1400407E-03 0.1947709 at 30iterations 1.0727767E-04 1.5335083E-02 at 40iterations 1.0134389E-05 1.6536713E-03 at 50iterations finished qdiffx linear iterations at : 18:30:52 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.0134389E-05 1.6536713E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 18:30:52 4.532u 0.414s 0:05.31 93.0% 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 18:30:52 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.870632 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 1.870632 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.19003 87.68142 89.91613 assigned negative charge : -387.4045 centred at (gu) : 84.87630 87.80666 89.58273 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 24942 mr = 50209 m= 3595 mr = 18657 m= 197 mr = 2322 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 9639 time to turn everything in is 0.7200000 number of dielectric boundary points 28639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 19249 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) : 0.6235440 object centre at (A) : -7.085501 -0.3245001 15.88150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4515921E-02 2.2109730E-02 midg,1,midg; midg,igrid,midg 1.2971218E-02 3.0945227E-03 1,midg,midg; igrid,midg,midg -8.7977313E-03 2.9743791E-02 gauss-seidel spectral radius is 0.9985783 estimated iterations to convergence 210 setup time was (sec) 1.040000 now iterating at: 18:30:54 rms-change max change #iterations 4.090310 167.7900 at 10iterations 1.881303 64.76747 at 20iterations 0.8690879 28.62785 at 30iterations 0.4005937 13.44616 at 40iterations 0.1848811 6.027776 at 50iterations 8.5607000E-02 2.704859 at 60iterations 3.9390825E-02 1.326061 at 70iterations 1.8253272E-02 0.6420898 at 80iterations 8.3796214E-03 0.2731018 at 90iterations 3.8704770E-03 0.1324272 at 100iterations 1.7865392E-03 5.3585052E-02 at 110iterations 8.2822016E-04 2.8005600E-02 at 120iterations finished qdiffx linear iterations at : 18:31:03 total time elapsed so far: 10.03000 # loops : 120 mean,max change (kT/e) : 8.2822016E-04 2.8005600E-02 energy calculations done at 10.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.24000 DelPhi exited at 18:31:03 10.244u 0.455s 0:10.97 97.4% 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 Sat Oct 8 2011 at 18:31:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.805948 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): -31.56400 17.39300 ymin,ymax (A): -23.55600 22.90700 zmin,zma (A): -12.66500 44.42800 x,y,z range (A): 48.95700 46.46300 57.09300 scale (grids/A): 2.805948 object centre (A): -7.085501 -0.3245001 15.88150 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.78505 86.52210 89.87418 assigned negative charge : -387.4045 centred at (gu) : 82.31439 86.70984 89.37406 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 164975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21178 grid for indexing accessible points = 1.400000 m= 82476 mr = 121359 m= 28244 mr = 68547 m= 6432 mr = 22967 m= 891 mr = 4912 m= 46 mr = 651 m= 0 mr = 20 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 32241 time to turn everything in is 1.860000 number of dielectric boundary points 64608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 19630 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) : 1.870632 object centre at (A) : -7.085501 -0.3245001 15.88150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1669711E-02 0.2054493 midg,1,midg; midg,igrid,midg 0.1508312 2.8355533E-02 1,midg,midg; igrid,midg,midg -6.4776413E-02 0.3985442 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 2.220000 now iterating at: 18:31:06 rms-change max change #iterations 9.532161 313.1301 at 10iterations 5.457528 114.2808 at 20iterations 3.110625 63.53030 at 30iterations 1.768963 36.58094 at 40iterations 1.008480 18.30794 at 50iterations 0.5737121 11.20353 at 60iterations 0.3264090 5.856056 at 70iterations 0.1858652 3.505041 at 80iterations 0.1058287 1.991240 at 90iterations 6.0094390E-02 1.161610 at 100iterations 3.4178097E-02 0.6191006 at 110iterations 1.9464657E-02 0.3483257 at 120iterations 1.1048325E-02 0.2191072 at 130iterations 6.2999041E-03 0.1197853 at 140iterations 3.5857556E-03 6.7127228E-02 at 150iterations 2.0371499E-03 4.7185898E-02 at 160iterations 1.1561088E-03 2.0130157E-02 at 170iterations 6.5783685E-04 1.3347626E-02 at 180iterations finished qdiffx linear iterations at : 18:31:21 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 6.5783685E-04 1.3347626E-02 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.76000 DelPhi exited at 18:31:22 17.766u 0.464s 0:18.50 98.4% 0+0k 0+0io 0pf+0w