Sat Oct 8 14:39:05 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 14:39:06 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: NAP 317 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: 0.6482038 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 0.6482038 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 1.4008060E-02 assigned positive charge : 456.4706 centred at (gu) : 91.44464 90.26913 89.76116 assigned negative charge : -456.4573 centred at (gu) : 91.35576 90.34248 89.79126 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8401 nv = 96 ne = 84 npr = 64177 no. pairs analyzed = 64177 no. exposed pairs = 3472 no. arc points = 24032 no. surface atoms = 1178 nbur = 1864 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4919 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2005782E-09 -5.0731965E-09 midg,1,midg; midg,igrid,midg 1.1554218E-08 -1.3578538E-08 1,midg,midg; igrid,midg,midg -1.1384120E-08 2.0338511E-08 gauss-seidel spectral radius is 0.9876987 estimated iterations to convergence 74 setup time was (sec) 0.6500000 now iterating at: 14:39:07 rms-change max change #iterations 0.1727282 21.74289 at 10iterations 1.7996527E-02 2.673481 at 20iterations 1.9104779E-03 0.2478650 at 30iterations 2.1853369E-04 2.8723717E-02 at 40iterations 2.8274908E-05 3.4332275E-03 at 50iterations finished qdiffx linear iterations at : 14:39:10 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 2.8274908E-05 3.4332275E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 14:39:11 4.664u 0.414s 0:05.50 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 Sat Oct 8 2011 at 14:39:11 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: NAP 317 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: 1.944611 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 1.944611 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 1.4008060E-02 assigned positive charge : 456.4706 centred at (gu) : 94.33349 90.80671 89.28292 assigned negative charge : -456.4573 centred at (gu) : 94.06692 91.02729 89.37343 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 91626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24032 grid for indexing accessible points = 1.400000 m= 32969 mr = 66290 m= 4987 mr = 24897 m= 285 mr = 3159 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 114 time to turn everything in is 0.7600000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22811 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) : 0.6482038 object centre at (A) : -3.097501 -8.6000443E-02 0.4065008 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8746110E-03 -1.4282800E-02 midg,1,midg; midg,igrid,midg 1.5698839E-02 2.5903909E-02 1,midg,midg; igrid,midg,midg -2.9201945E-02 2.3882782E-02 gauss-seidel spectral radius is 0.9987221 estimated iterations to convergence 222 setup time was (sec) 1.040000 now iterating at: 14:39:13 rms-change max change #iterations 4.900139 221.9962 at 10iterations 2.364449 69.97263 at 20iterations 1.131407 32.41648 at 30iterations 0.5447304 15.95181 at 40iterations 0.2615762 7.298149 at 50iterations 0.1253931 3.658787 at 60iterations 6.0472887E-02 1.675832 at 70iterations 2.9103441E-02 0.8915195 at 80iterations 1.4007675E-02 0.3901128 at 90iterations 6.7555304E-03 0.2116241 at 100iterations 3.2475563E-03 0.1110001 at 110iterations 1.5634476E-03 4.6704292E-02 at 120iterations finished qdiffx linear iterations at : 14:39:24 total time elapsed so far: 11.95000 # loops : 120 mean,max change (kT/e) : 1.5634476E-03 4.6704292E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 14:39:25 12.122u 0.707s 0:13.67 93.7% 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 14:39:25 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: NAP 317 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: 2.916917 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 2.916917 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 1.4008060E-02 assigned positive charge : 456.4706 centred at (gu) : 96.50007 91.21016 88.92431 assigned negative charge : -456.4573 centred at (gu) : 96.10024 91.54093 89.05999 start vw surface at 0.1200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 212457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24032 grid for indexing accessible points = 1.400000 m= 108435 mr = 160189 m= 38289 mr = 90527 m= 8729 mr = 31097 m= 1254 mr = 6647 m= 73 mr = 832 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 363 time to turn everything in is 1.990000 number of dielectric boundary points 79920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 23158 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) : 1.944611 object centre at (A) : -3.097501 -8.6000443E-02 0.4065008 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4116284E-02 -0.1215165 midg,1,midg; midg,igrid,midg 4.8180673E-02 0.3089994 1,midg,midg; igrid,midg,midg -0.1614289 0.3115191 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 2.390000 now iterating at: 14:39:28 rms-change max change #iterations 11.20519 412.6140 at 10iterations 6.587951 143.3779 at 20iterations 3.867016 77.92644 at 30iterations 2.261876 45.80597 at 40iterations 1.321474 22.46603 at 50iterations 0.7732182 13.84939 at 60iterations 0.4498797 7.492859 at 70iterations 0.2616299 4.437200 at 80iterations 0.1519445 2.556198 at 90iterations 8.8642046E-02 1.478777 at 100iterations 5.1543191E-02 0.8087978 at 110iterations 2.9891131E-02 0.4860840 at 120iterations 1.7407261E-02 0.2740860 at 130iterations 1.0127025E-02 0.1605759 at 140iterations 5.9131426E-03 9.2578888E-02 at 150iterations 3.4549874E-03 5.7328224E-02 at 160iterations 2.0311188E-03 3.6560059E-02 at 170iterations 1.2015060E-03 1.8857956E-02 at 180iterations finished qdiffx linear iterations at : 14:39:45 total time elapsed so far: 19.45000 # loops : 180 mean,max change (kT/e) : 1.2015060E-03 1.8857956E-02 energy calculations done at 19.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.63000 DelPhi exited at 14:39:46 19.633u 0.616s 0:21.12 95.8% 0+0k 0+0io 0pf+0w