Sat Oct 8 14:02:54 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 14:02:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 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: 0.6401841 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): -12.39000 43.21900 ymin,ymax (A): -22.25300 22.58200 zmin,zma (A): -7.429000 47.87700 x,y,z range (A): 55.60900 44.83500 55.30600 scale (grids/A): 0.6401841 object centre (A): 15.41450 0.1644993 20.22400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 88.77427 89.57735 91.56339 assigned negative charge : -455.8243 centred at (gu) : 88.75944 89.47609 91.47318 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8202 nv = 96 ne = 84 npr = 63789 no. pairs analyzed = 63789 no. exposed pairs = 3451 no. arc points = 24129 no. surface atoms = 1180 nbur = 1863 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 4780 m= 4 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2377 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 10108 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9862624E-09 1.7128180E-08 midg,1,midg; midg,igrid,midg -1.5522529E-08 1.2427060E-08 1,midg,midg; igrid,midg,midg -2.8115601E-09 1.4726871E-09 gauss-seidel spectral radius is 0.9873902 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 14:02:55 rms-change max change #iterations 0.1595377 26.18203 at 10iterations 1.6226910E-02 2.361099 at 20iterations 1.6303863E-03 0.1947231 at 30iterations 1.7736753E-04 2.6968002E-02 at 40iterations 2.1393053E-05 3.4179688E-03 at 50iterations finished qdiffx linear iterations at : 14:02:59 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 2.1393053E-05 3.4179688E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:02:59 4.230u 0.249s 0:04.87 91.7% 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 14:02:59 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 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: 1.920552 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): -12.39000 43.21900 ymin,ymax (A): -22.25300 22.58200 zmin,zma (A): -7.429000 47.87700 x,y,z range (A): 55.60900 44.83500 55.30600 scale (grids/A): 1.920552 object centre (A): 15.41450 0.1644993 20.22400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 86.32224 88.73154 94.68938 assigned negative charge : -455.8243 centred at (gu) : 86.27793 88.42834 94.41933 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24129 grid for indexing accessible points = 1.400000 m= 32830 mr = 64916 m= 4796 mr = 24849 m= 307 mr = 2957 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.6400000 number of dielectric boundary points 34939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22770 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) : 0.6401841 object centre at (A) : 15.41450 0.1644993 20.22400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5671318E-02 2.4812538E-02 midg,1,midg; midg,igrid,midg -2.1465719E-03 2.0949198E-02 1,midg,midg; igrid,midg,midg -4.0147290E-02 1.7732760E-02 gauss-seidel spectral radius is 0.9986916 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 14:03:01 rms-change max change #iterations 4.742943 199.2469 at 10iterations 2.263857 81.02490 at 20iterations 1.079392 39.38049 at 30iterations 0.5149190 15.16953 at 40iterations 0.2445980 7.109353 at 50iterations 0.1167143 3.358437 at 60iterations 5.5710636E-02 1.587749 at 70iterations 2.6532216E-02 0.7365198 at 80iterations 1.2692925E-02 0.3457298 at 90iterations 6.0509900E-03 0.1767335 at 100iterations 2.8826862E-03 8.6379051E-02 at 110iterations 1.3800921E-03 3.8970947E-02 at 120iterations finished qdiffx linear iterations at : 14:03:09 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 1.3800921E-03 3.8970947E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 14:03:10 9.821u 0.282s 0:10.40 97.1% 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 14:03:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: NAP 500 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: 2.880829 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): -12.39000 43.21900 ymin,ymax (A): -22.25300 22.58200 zmin,zma (A): -7.429000 47.87700 x,y,z range (A): 55.60900 44.83500 55.30600 scale (grids/A): 2.880829 object centre (A): 15.41450 0.1644993 20.22400 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 84.48323 88.09721 97.03393 assigned negative charge : -455.8243 centred at (gu) : 84.41697 87.64246 96.62896 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 208335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24129 grid for indexing accessible points = 1.400000 m= 107050 mr = 156927 m= 37634 mr = 89395 m= 8723 mr = 30585 m= 1276 mr = 6438 m= 78 mr = 872 m= 0 mr = 41 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 516 time to turn everything in is 1.700000 number of dielectric boundary points 78838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 23167 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) : 1.920552 object centre at (A) : 15.41450 0.1644993 20.22400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2985968E-02 0.3615889 midg,1,midg; midg,igrid,midg -1.2151098E-02 0.2428610 1,midg,midg; igrid,midg,midg -0.6238788 0.3027354 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 2.070000 now iterating at: 14:03:12 rms-change max change #iterations 10.97985 441.4178 at 10iterations 6.457572 159.5681 at 20iterations 3.781008 69.16502 at 30iterations 2.205706 38.04942 at 40iterations 1.283927 24.27937 at 50iterations 0.7489876 14.74488 at 60iterations 0.4339944 7.123070 at 70iterations 0.2521780 4.621849 at 80iterations 0.1461648 2.446970 at 90iterations 8.4884599E-02 1.444300 at 100iterations 4.9114492E-02 0.8193035 at 110iterations 2.8446835E-02 0.5076991 at 120iterations 1.6498465E-02 0.2631295 at 130iterations 9.5638065E-03 0.1535780 at 140iterations 5.5442569E-03 9.4371796E-02 at 150iterations 3.2213461E-03 5.3821564E-02 at 160iterations 1.8753732E-03 3.4442425E-02 at 170iterations 1.0955769E-03 1.7570496E-02 at 180iterations finished qdiffx linear iterations at : 14:03:26 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 1.0955769E-03 1.7570496E-02 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 14:03:26 15.945u 0.266s 0:16.49 98.2% 0+0k 0+0io 0pf+0w