Tue Oct 11 08:25:44 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 Tue Oct 11 2011 at 08:25:44 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6586007 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 0.6586007 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 90.10201 90.41856 88.97911 assigned negative charge : -436.8902 centred at (gu) : 90.35507 90.31547 88.98196 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8365 nv = 96 ne = 84 npr = 59278 no. pairs analyzed = 59278 no. exposed pairs = 3524 no. arc points = 24275 no. surface atoms = 1181 nbur = 1713 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4764 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3400000 number of dielectric boundary points 3986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2390 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3086981E-09 3.8504995E-09 midg,1,midg; midg,igrid,midg -1.5576372E-08 2.9731074E-08 1,midg,midg; igrid,midg,midg 5.6981055E-08 -5.1614229E-08 gauss-seidel spectral radius is 0.9880743 estimated iterations to convergence 75 setup time was (sec) 0.6000000 now iterating at: 08:25:45 rms-change max change #iterations 0.1717495 24.27668 at 10iterations 1.8917177E-02 2.717613 at 20iterations 2.1194317E-03 0.2353487 at 30iterations 2.8960136E-04 3.6071777E-02 at 40iterations 6.2563748E-05 8.6212158E-03 at 50iterations finished qdiffx linear iterations at : 08:25:49 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 6.2563748E-05 8.6212158E-03 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 08:25:50 4.771u 0.385s 0:05.45 94.4% 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 Tue Oct 11 2011 at 08:25:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.975802 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 1.975802 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 90.30506 91.25501 86.93671 assigned negative charge : -436.8902 centred at (gu) : 91.06506 90.94597 86.94530 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 34372 mr = 64267 m= 5776 mr = 25931 m= 405 mr = 3672 m= 3 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 0.7400000 number of dielectric boundary points 36770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21644 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) : 0.6586007 object centre at (A) : 9.537501 31.16000 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6086699E-03 -2.7419478E-02 midg,1,midg; midg,igrid,midg -5.1648729E-03 1.9141579E-02 1,midg,midg; igrid,midg,midg 7.7355385E-02 -1.4113038E-02 gauss-seidel spectral radius is 0.9987567 estimated iterations to convergence 225 setup time was (sec) 1.050000 now iterating at: 08:25:51 rms-change max change #iterations 4.861341 243.5745 at 10iterations 2.361861 75.61195 at 20iterations 1.147137 32.35521 at 30iterations 0.5592114 15.48660 at 40iterations 0.2723069 8.334977 at 50iterations 0.1320937 3.738775 at 60iterations 6.4229824E-02 1.836618 at 70iterations 3.1259015E-02 0.9556274 at 80iterations 1.5166242E-02 0.4275780 at 90iterations 7.4017495E-03 0.2354889 at 100iterations 3.6153710E-03 0.1010742 at 110iterations 1.7823796E-03 5.1086426E-02 at 120iterations finished qdiffx linear iterations at : 08:26:02 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 1.7823796E-03 5.1086426E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 08:26:03 12.026u 0.439s 0:13.08 95.1% 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 Tue Oct 11 2011 at 08:26:03 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.963703 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 2.963703 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 90.45753 91.88255 85.40496 assigned negative charge : -436.8902 centred at (gu) : 91.59757 91.41880 85.41787 start vw surface at 0.1200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 208395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 110274 mr = 154756 m= 41408 mr = 91693 m= 10398 mr = 33763 m= 1697 mr = 7894 m= 130 mr = 1219 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 3706 time to turn everything in is 1.970000 number of dielectric boundary points 82923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 21927 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) : 1.975802 object centre at (A) : 9.537501 31.16000 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1243284 -0.3413408 midg,1,midg; midg,igrid,midg -6.7067035E-02 0.2333612 1,midg,midg; igrid,midg,midg 0.6688467 -0.1112309 gauss-seidel spectral radius is 0.9992920 estimated iterations to convergence 297 setup time was (sec) 2.320000 now iterating at: 08:26:06 rms-change max change #iterations 11.16640 364.5814 at 10iterations 6.590896 170.6664 at 20iterations 3.880066 85.60270 at 30iterations 2.277048 43.52246 at 40iterations 1.336462 23.88674 at 50iterations 0.7847108 15.76437 at 60iterations 0.4593579 8.089244 at 70iterations 0.2685767 4.458086 at 80iterations 0.1568774 3.054530 at 90iterations 9.1531821E-02 1.535950 at 100iterations 5.3524282E-02 0.9840374 at 110iterations 3.1226691E-02 0.5431290 at 120iterations 1.8258667E-02 0.2864380 at 130iterations 1.0688478E-02 0.1796303 at 140iterations 6.2759882E-03 0.1122475 at 150iterations 3.7001914E-03 5.9326172E-02 at 160iterations 2.1955399E-03 4.1742325E-02 at 170iterations 1.3238668E-03 2.2048950E-02 at 180iterations finished qdiffx linear iterations at : 08:26:25 total time elapsed so far: 21.19000 # loops : 180 mean,max change (kT/e) : 1.3238668E-03 2.2048950E-02 energy calculations done at 21.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.35000 DelPhi exited at 08:26:25 21.354u 0.467s 0:22.16 98.4% 0+0k 0+0io 0pf+0w