Wed Dec 28 11:02:29 PST 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 Wed Dec 28 2011 at 11:02:29 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 = 1972 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: 0.5598276 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 0.5598276 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000003 assigned positive charge : 289.1841 centred at (gu) : 89.62108 90.09738 89.99776 assigned negative charge : -285.1843 centred at (gu) : 89.71053 89.95096 89.99870 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4088 nv = 96 ne = 84 npr = 40054 no. pairs analyzed = 40054 no. exposed pairs = 2492 no. arc points = 18009 no. surface atoms = 838 nbur = 1134 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 142 mr = 2154 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2714013E-10 4.1343193E-10 midg,1,midg; midg,igrid,midg -6.1848882E-10 1.4716093E-09 1,midg,midg; igrid,midg,midg 1.1463511E-09 -1.9804784E-10 gauss-seidel spectral radius is 0.9834602 estimated iterations to convergence 64 setup time was (sec) 0.7200000 now iterating at: 11:02:31 rms-change max change #iterations 6.5859579E-02 16.11651 at 10iterations 4.7656884E-03 0.9293594 at 20iterations 3.3076410E-04 6.1702728E-02 at 30iterations 2.3112720E-05 4.1503906E-03 at 40iterations 1.6626307E-06 3.2997131E-04 at 50iterations finished qdiffx linear iterations at : 11:02:38 total time elapsed so far: 7.360000 # loops : 50 mean,max change (kT/e) : 1.6626307E-06 3.2997131E-04 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 11:02:40 7.532u 0.776s 0:10.28 80.7% 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 Wed Dec 28 2011 at 11:02:40 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 = 1972 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: 1.679483 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 1.679483 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000003 assigned positive charge : 289.1841 centred at (gu) : 88.86315 90.29224 89.99321 assigned negative charge : -285.1843 centred at (gu) : 89.13178 89.85317 89.99623 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 45109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14172 mr = 30433 m= 1428 mr = 10374 m= 41 mr = 716 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 612 time to turn everything in is 0.4800000 number of dielectric boundary points 19227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14207 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) : 0.5598276 object centre at (A) : -19.17300 34.18150 27.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1131830E-02 2.0106703E-02 midg,1,midg; midg,igrid,midg -4.3673036E-03 2.9904887E-03 1,midg,midg; igrid,midg,midg -3.1007151E-04 -9.0782938E-04 gauss-seidel spectral radius is 0.9981673 estimated iterations to convergence 186 setup time was (sec) 1.020000 now iterating at: 11:02:41 rms-change max change #iterations 2.724183 157.2957 at 10iterations 1.127548 49.20826 at 20iterations 0.4669509 18.94543 at 30iterations 0.1940802 8.915380 at 40iterations 8.0261737E-02 3.188434 at 50iterations 3.3403881E-02 1.386276 at 60iterations 1.3967169E-02 0.6778178 at 70iterations 5.7923850E-03 0.2389526 at 80iterations 2.3945021E-03 0.1032219 at 90iterations 9.9122152E-04 4.0763855E-02 at 100iterations 4.1304398E-04 1.7005920E-02 at 110iterations 1.7170623E-04 7.1029663E-03 at 120iterations finished qdiffx linear iterations at : 11:02:59 total time elapsed so far: 18.89000 # loops : 120 mean,max change (kT/e) : 1.7170623E-04 7.1029663E-03 energy calculations done at 18.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.07000 DelPhi exited at 11:03:01 19.075u 0.805s 0:21.26 93.4% 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 Wed Dec 28 2011 at 11:03:01 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 = 1972 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: 2.519224 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): -42.01200 3.666000 ymin,ymax (A): 13.78800 54.57500 zmin,zma (A): -4.486000 59.10500 x,y,z range (A): 45.67800 40.78700 63.59100 scale (grids/A): 2.519224 object centre (A): -19.17300 34.18150 27.30950 number of atom coordinates read : 1972 total number of charged atoms : 1840 net assigned charge : 4.000003 assigned positive charge : 289.1841 centred at (gu) : 88.29472 90.43830 89.98989 assigned negative charge : -285.1843 centred at (gu) : 88.69773 89.77982 89.99445 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 104542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 49152 mr = 74103 m= 14316 mr = 40131 m= 2208 mr = 11288 m= 140 mr = 1421 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2225 time to turn everything in is 1.120000 number of dielectric boundary points 43363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14704 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) : 1.679483 object centre at (A) : -19.17300 34.18150 27.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2117580 0.2007042 midg,1,midg; midg,igrid,midg -6.0974721E-02 1.1053342E-02 1,midg,midg; igrid,midg,midg -3.3479538E-02 -1.8515777E-02 gauss-seidel spectral radius is 0.9990982 estimated iterations to convergence 263 setup time was (sec) 1.670000 now iterating at: 11:03:04 rms-change max change #iterations 6.911162 361.9916 at 10iterations 3.767637 110.3592 at 20iterations 2.050541 63.26349 at 30iterations 1.114480 29.77506 at 40iterations 0.6035222 16.20505 at 50iterations 0.3262255 7.747828 at 60iterations 0.1765013 4.777965 at 70iterations 9.5416874E-02 2.200043 at 80iterations 5.1581662E-02 1.329309 at 90iterations 2.7861657E-02 0.6897278 at 100iterations 1.5050341E-02 0.4017715 at 110iterations 8.1379116E-03 0.2057457 at 120iterations 4.4047874E-03 0.1021175 at 130iterations 2.3821802E-03 6.0089111E-02 at 140iterations 1.2883216E-03 3.2449961E-02 at 150iterations 6.9424603E-04 1.6536713E-02 at 160iterations 3.7580292E-04 8.8958740E-03 at 170iterations 2.0264357E-04 4.8675537E-03 at 180iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 29.76000 # loops : 180 mean,max change (kT/e) : 2.0264357E-04 4.8675537E-03 energy calculations done at 29.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.94000 DelPhi exited at 11:03:33 29.947u 0.844s 0:32.26 95.4% 0+0k 0+0io 0pf+0w