Mon Oct 10 12:12:21 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 Mon Oct 10 2011 at 12:12:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7469262 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 0.7469262 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.40179 90.48270 90.02333 assigned negative charge : -323.3720 centred at (gu) : 89.41603 90.57322 90.20493 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8198 nv = 96 ne = 84 npr = 43252 no. pairs analyzed = 43252 no. exposed pairs = 2715 no. arc points = 19166 no. surface atoms = 922 nbur = 1195 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 607 mr = 4587 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.2800000 number of dielectric boundary points 4102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2847599E-08 -3.4707693E-07 midg,1,midg; midg,igrid,midg -2.0294962E-08 -2.5715562E-07 1,midg,midg; igrid,midg,midg -1.2305260E-07 -1.2961199E-07 gauss-seidel spectral radius is 0.9906608 estimated iterations to convergence 84 setup time was (sec) 0.6000000 now iterating at: 12:12:22 rms-change max change #iterations 0.2596374 36.83102 at 10iterations 3.5623312E-02 4.541729 at 20iterations 4.9137832E-03 0.5547523 at 30iterations 6.6982349E-04 8.4558487E-02 at 40iterations 9.0055379E-05 1.0101318E-02 at 50iterations finished qdiffx linear iterations at : 12:12:26 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 9.0055379E-05 1.0101318E-02 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 12:12:27 4.643u 0.375s 0:05.42 92.4% 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 Mon Oct 10 2011 at 12:12:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.240779 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 2.240779 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.20531 91.44786 90.07005 assigned negative charge : -323.3720 centred at (gu) : 88.24805 91.71964 90.61478 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19166 grid for indexing accessible points = 1.400000 m= 35285 mr = 58920 m= 8058 mr = 27081 m= 899 mr = 5642 m= 29 mr = 491 m= 0 mr = 2 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 0.7100000 number of dielectric boundary points 37575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15773 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) : 0.7469262 object centre at (A) : 32.18100 13.67500 20.46700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2830135E-03 -0.1303081 midg,1,midg; midg,igrid,midg -3.0929038E-02 -5.0201297E-02 1,midg,midg; igrid,midg,midg -1.7336807E-03 -4.2171814E-03 gauss-seidel spectral radius is 0.9989454 estimated iterations to convergence 244 setup time was (sec) 1.010000 now iterating at: 12:12:28 rms-change max change #iterations 5.221939 231.1827 at 10iterations 2.661854 82.02779 at 20iterations 1.365071 40.69252 at 30iterations 0.6990935 19.29149 at 40iterations 0.3581143 11.35153 at 50iterations 0.1841234 5.227444 at 60iterations 9.4417997E-02 2.614209 at 70iterations 4.8304785E-02 1.359581 at 80iterations 2.4800984E-02 0.7030628 at 90iterations 1.2778531E-02 0.3764839 at 100iterations 6.5300851E-03 0.1898241 at 110iterations 3.3490807E-03 8.7711334E-02 at 120iterations finished qdiffx linear iterations at : 12:12:38 total time elapsed so far: 10.99000 # loops : 120 mean,max change (kT/e) : 3.3490807E-03 8.7711334E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 12:12:39 11.154u 0.479s 0:12.02 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 Mon Oct 10 2011 at 12:12:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.361168 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): 8.350000 56.01200 ymin,ymax (A): -8.983000 36.33300 zmin,zma (A): -3.240000 44.17400 x,y,z range (A): 47.66200 45.31600 47.41400 scale (grids/A): 3.361168 object centre (A): 32.18100 13.67500 20.46700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.30782 92.17172 90.10514 assigned negative charge : -323.3720 centred at (gu) : 87.37208 92.57937 90.92210 start vw surface at 0.1000000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 196688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19166 grid for indexing accessible points = 1.400000 m= 106222 mr = 141766 m= 47140 mr = 88235 m= 15585 mr = 39532 m= 3765 mr = 12483 m= 503 mr = 2922 m= 17 mr = 301 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 2858 time to turn everything in is 2.280000 number of dielectric boundary points 84681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.410000 number of grid points assigned charge 15824 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) : 2.240779 object centre at (A) : 32.18100 13.67500 20.46700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4547658E-02 -1.229554 midg,1,midg; midg,igrid,midg -0.2719851 -0.2506841 1,midg,midg; igrid,midg,midg -6.0450066E-02 -0.1019377 gauss-seidel spectral radius is 0.9993221 estimated iterations to convergence 303 setup time was (sec) 2.620000 now iterating at: 12:12:42 rms-change max change #iterations 11.05691 316.0123 at 10iterations 6.520370 119.6447 at 20iterations 3.854134 71.08836 at 30iterations 2.271439 44.48096 at 40iterations 1.339049 23.80788 at 50iterations 0.7890044 13.08319 at 60iterations 0.4648598 7.615149 at 70iterations 0.2732051 4.595402 at 80iterations 0.1609835 2.516319 at 90iterations 9.4655454E-02 1.518126 at 100iterations 5.5565443E-02 0.8690138 at 110iterations 3.2701489E-02 0.5462503 at 120iterations 1.9259576E-02 0.2867565 at 130iterations 1.1303998E-02 0.1747169 at 140iterations 6.6658650E-03 0.1094551 at 150iterations 3.9159879E-03 6.5732956E-02 at 160iterations 2.3008594E-03 3.8657188E-02 at 170iterations 1.3540871E-03 2.2003174E-02 at 180iterations finished qdiffx linear iterations at : 12:13:11 total time elapsed so far: 31.61000 # loops : 180 mean,max change (kT/e) : 1.3540871E-03 2.2003174E-02 energy calculations done at 31.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.79000 DelPhi exited at 12:13:12 31.796u 0.627s 0:32.81 98.7% 0+0k 0+0io 0pf+0w