Tue Oct 11 08:08:48 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 Tue Oct 11 2011 at 08:08:48 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2308 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6400231 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 0.6400231 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500027 assigned positive charge : 349.0903 centred at (gu) : 90.34917 87.76449 92.03419 assigned negative charge : -341.5908 centred at (gu) : 90.22784 87.73415 91.97475 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6425 nv = 96 ne = 84 npr = 45939 no. pairs analyzed = 45939 no. exposed pairs = 3082 no. arc points = 21716 no. surface atoms = 1030 nbur = 1278 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3319 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2198 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7672 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1555936E-09 2.5798878E-08 midg,1,midg; midg,igrid,midg 1.2023017E-08 8.6980556E-09 1,midg,midg; igrid,midg,midg -1.6119344E-09 2.4657446E-08 gauss-seidel spectral radius is 0.9873320 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 08:08:49 rms-change max change #iterations 0.1365321 26.67422 at 10iterations 1.3538398E-02 1.915613 at 20iterations 1.3832006E-03 0.2201920 at 30iterations 1.6364954E-04 3.0999184E-02 at 40iterations 3.7499405E-05 8.2244873E-03 at 50iterations finished qdiffx linear iterations at : 08:08:52 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 3.7499405E-05 8.2244873E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 08:08:53 4.049u 0.245s 0:04.94 86.6% 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 Tue Oct 11 2011 at 08:08:53 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2308 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920069 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 1.920069 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500027 assigned positive charge : 349.0903 centred at (gu) : 91.04733 83.29314 96.10223 assigned negative charge : -341.5908 centred at (gu) : 90.68343 83.20227 95.92429 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21716 grid for indexing accessible points = 1.400000 m= 24337 mr = 47003 m= 3704 mr = 17243 m= 224 mr = 2070 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17134 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) : 0.6400231 object centre at (A) : 3.194000 49.91350 27.01450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0796225E-04 3.6041185E-02 midg,1,midg; midg,igrid,midg 5.3105086E-02 4.7527142E-02 1,midg,midg; igrid,midg,midg -5.9982473E-03 2.9476827E-02 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.9200000 now iterating at: 08:08:54 rms-change max change #iterations 4.032398 175.5771 at 10iterations 1.879786 73.80280 at 20iterations 0.8735607 27.26937 at 30iterations 0.4082976 16.43924 at 40iterations 0.1905949 6.532465 at 50iterations 8.8780530E-02 3.114008 at 60iterations 4.1465629E-02 1.358036 at 70iterations 1.9330850E-02 0.6799173 at 80iterations 9.0325652E-03 0.3159504 at 90iterations 4.2088041E-03 0.1408396 at 100iterations 1.9768404E-03 6.2011719E-02 at 110iterations 9.3601918E-04 3.1501770E-02 at 120iterations finished qdiffx linear iterations at : 08:09:03 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 9.3601918E-04 3.1501770E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 08:09:03 9.372u 0.315s 0:10.07 96.1% 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 08:09:03 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2308 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.880104 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): -22.73100 29.11900 ymin,ymax (A): 22.10200 77.72500 zmin,zma (A): 2.230000 51.79900 x,y,z range (A): 51.85000 55.62300 49.56900 scale (grids/A): 2.880104 object centre (A): 3.194000 49.91350 27.01450 number of atom coordinates read : 2308 total number of charged atoms : 2172 net assigned charge : 7.500027 assigned positive charge : 349.0903 centred at (gu) : 91.57082 79.93953 99.15331 assigned negative charge : -341.5908 centred at (gu) : 91.02515 79.80344 98.88634 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 160887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21716 grid for indexing accessible points = 1.400000 m= 79175 mr = 114148 m= 27763 mr = 63339 m= 6455 mr = 21550 m= 950 mr = 4461 m= 69 mr = 582 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 71185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 17375 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) : 1.920069 object centre at (A) : 3.194000 49.91350 27.01450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6454978E-02 0.3411112 midg,1,midg; midg,igrid,midg 0.4836066 0.7606426 1,midg,midg; igrid,midg,midg -3.4785680E-02 0.4651739 gauss-seidel spectral radius is 0.9992611 estimated iterations to convergence 290 setup time was (sec) 1.920000 now iterating at: 08:09:06 rms-change max change #iterations 9.653911 474.9397 at 10iterations 5.702108 135.7540 at 20iterations 3.335215 77.44677 at 30iterations 1.940879 45.25069 at 40iterations 1.127469 26.32716 at 50iterations 0.6536397 16.14800 at 60iterations 0.3783320 10.39850 at 70iterations 0.2188359 4.452448 at 80iterations 0.1260537 2.394110 at 90iterations 7.2731420E-02 1.340974 at 100iterations 4.1752622E-02 0.7702045 at 110iterations 2.4120359E-02 0.4580998 at 120iterations 1.3858972E-02 0.2926545 at 130iterations 8.0010034E-03 0.1552429 at 140iterations 4.6222769E-03 8.8169098E-02 at 150iterations 2.6749033E-03 5.7687759E-02 at 160iterations 1.5592778E-03 3.1561375E-02 at 170iterations 9.2254533E-04 1.9577026E-02 at 180iterations finished qdiffx linear iterations at : 08:09:20 total time elapsed so far: 15.91000 # loops : 180 mean,max change (kT/e) : 9.2254533E-04 1.9577026E-02 energy calculations done at 15.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 08:09:21 16.082u 0.328s 0:17.17 95.5% 0+0k 0+0io 0pf+0w