Sat Oct 8 21:39:59 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 21:39:59 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6620176 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 0.6620176 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 87.82616 89.36703 88.96713 assigned negative charge : -302.7228 centred at (gu) : 87.94141 89.40415 89.00422 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6030 nv = 96 ne = 84 npr = 40360 no. pairs analyzed = 40360 no. exposed pairs = 2652 no. arc points = 18530 no. surface atoms = 887 nbur = 1138 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3253 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1664 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4857613E-09 -5.4569136E-09 midg,1,midg; midg,igrid,midg 5.9578888E-09 -5.9378662E-09 1,midg,midg; igrid,midg,midg 2.8108056E-08 -1.2449586E-08 gauss-seidel spectral radius is 0.9881232 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 21:39:59 rms-change max change #iterations 0.1493084 25.43856 at 10iterations 1.5746700E-02 2.774811 at 20iterations 1.7015982E-03 0.2505102 at 30iterations 1.8277742E-04 3.3473969E-02 at 40iterations 2.1841890E-05 3.3369064E-03 at 50iterations finished qdiffx linear iterations at : 21:40:02 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.1841890E-05 3.3369064E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 21:40:03 3.318u 0.173s 0:03.76 92.5% 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 Sat Oct 8 2011 at 21:40:03 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.986053 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 1.986053 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 83.47820 88.10114 86.90142 assigned negative charge : -302.7228 centred at (gu) : 83.82407 88.21234 87.01274 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18530 grid for indexing accessible points = 1.400000 m= 23673 mr = 44178 m= 4127 mr = 17196 m= 294 mr = 2583 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 251 time to turn everything in is 0.3200000 number of dielectric boundary points 28625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14911 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) : 0.6620176 object centre at (A) : 32.82450 26.57450 35.35250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4981527E-03 -2.3228636E-03 midg,1,midg; midg,igrid,midg 2.3030078E-02 1.2239218E-03 1,midg,midg; igrid,midg,midg -4.1245464E-02 -4.3894239E-02 gauss-seidel spectral radius is 0.9986840 estimated iterations to convergence 218 setup time was (sec) 0.5300000 now iterating at: 21:40:03 rms-change max change #iterations 4.051059 222.7805 at 10iterations 1.926008 70.43066 at 20iterations 0.9121382 33.08150 at 30iterations 0.4336063 14.91476 at 40iterations 0.2062599 6.980538 at 50iterations 9.7826019E-02 3.175142 at 60iterations 4.6261225E-02 1.544741 at 70iterations 2.2042869E-02 0.7484725 at 80iterations 1.0481265E-02 0.3476219 at 90iterations 4.9870266E-03 0.1636162 at 100iterations 2.3739825E-03 8.0862045E-02 at 110iterations 1.1252573E-03 4.1839600E-02 at 120iterations finished qdiffx linear iterations at : 21:40:10 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.1252573E-03 4.1839600E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 21:40:11 7.620u 0.200s 0:08.09 96.6% 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 21:40:11 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2025 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.979079 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): 5.937000 59.71200 ymin,ymax (A): 2.951000 50.19800 zmin,zma (A): 14.67600 56.02900 x,y,z range (A): 53.77500 47.24700 41.35300 scale (grids/A): 2.979079 object centre (A): 32.82450 26.57450 35.35250 number of atom coordinates read : 2025 total number of charged atoms : 1885 net assigned charge : -7.9996467E-02 assigned positive charge : 302.6428 centred at (gu) : 80.21732 87.15164 85.35197 assigned negative charge : -302.7228 centred at (gu) : 80.73615 87.31853 85.51909 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 149262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18530 grid for indexing accessible points = 1.400000 m= 75199 mr = 107097 m= 28482 mr = 60875 m= 7608 mr = 22714 m= 1332 mr = 5732 m= 86 mr = 914 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 744 time to turn everything in is 0.8400000 number of dielectric boundary points 64606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 15080 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) : 1.986053 object centre at (A) : 32.82450 26.57450 35.35250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7757649E-02 -2.4326649E-02 midg,1,midg; midg,igrid,midg 0.2285641 -6.4095549E-02 1,midg,midg; igrid,midg,midg -0.6533861 -0.5804473 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.070000 now iterating at: 21:40:12 rms-change max change #iterations 9.459868 411.7017 at 10iterations 5.573388 136.5594 at 20iterations 3.259838 86.30040 at 30iterations 1.901819 40.43377 at 40iterations 1.106953 21.79692 at 50iterations 0.6432026 13.42884 at 60iterations 0.3723057 7.800310 at 70iterations 0.2159728 4.573030 at 80iterations 0.1243883 2.437623 at 90iterations 7.2038405E-02 1.344971 at 100iterations 4.1485488E-02 0.7607422 at 110iterations 2.3949575E-02 0.4435272 at 120iterations 1.3803327E-02 0.2585869 at 130iterations 7.9943938E-03 0.1518021 at 140iterations 4.6037207E-03 9.6862555E-02 at 150iterations 2.6758935E-03 5.2898407E-02 at 160iterations 1.5537554E-03 2.8663635E-02 at 170iterations 9.0532470E-04 1.8356323E-02 at 180iterations finished qdiffx linear iterations at : 21:40:23 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 9.0532470E-04 1.8356323E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 21:40:23 12.201u 0.205s 0:12.70 97.6% 0+0k 0+0io 0pf+0w