Sun Oct 9 13:02:31 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 Sun Oct 9 2011 at 13:02:31 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6828689 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 0.6828689 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2212 net assigned charge : 4.406012 assigned positive charge : 359.9892 centred at (gu) : 89.69544 90.84006 90.52421 assigned negative charge : -355.5836 centred at (gu) : 89.69791 90.95425 90.57430 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7570 nv = 96 ne = 84 npr = 46620 no. pairs analyzed = 46620 no. exposed pairs = 3014 no. arc points = 21353 no. surface atoms = 1015 nbur = 1342 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4152 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 3820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1991 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3092054E-08 5.1590190E-09 midg,1,midg; midg,igrid,midg 4.8018990E-08 -1.9344677E-08 1,midg,midg; igrid,midg,midg 2.2936097E-08 1.8890553E-08 gauss-seidel spectral radius is 0.9888614 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 13:02:32 rms-change max change #iterations 0.1846935 30.49617 at 10iterations 2.1494338E-02 2.753235 at 20iterations 3.0193017E-03 0.4021034 at 30iterations 7.0062547E-04 0.1088409 at 40iterations 2.2434717E-04 3.6190033E-02 at 50iterations finished qdiffx linear iterations at : 13:02:35 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.2434717E-04 3.6190033E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:02:35 3.393u 0.183s 0:03.84 92.9% 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 Sun Oct 9 2011 at 13:02:35 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.048607 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 2.048607 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2212 net assigned charge : 4.406012 assigned positive charge : 359.9892 centred at (gu) : 89.08582 92.51962 91.57217 assigned negative charge : -355.5836 centred at (gu) : 89.09345 92.86260 91.72269 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21353 grid for indexing accessible points = 1.400000 m= 31435 mr = 55040 m= 5671 mr = 23470 m= 468 mr = 3641 m= 6 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 0.4000000 number of dielectric boundary points 34935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17518 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) : 0.6828689 object centre at (A) : 18.79450 11.88950 23.93350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2124163E-02 9.8254588E-03 midg,1,midg; midg,igrid,midg 1.2350232E-02 -3.2862227E-02 1,midg,midg; igrid,midg,midg 5.1778290E-02 -8.7120122E-04 gauss-seidel spectral radius is 0.9987951 estimated iterations to convergence 228 setup time was (sec) 0.6200000 now iterating at: 13:02:36 rms-change max change #iterations 4.699296 201.6973 at 10iterations 2.287658 79.57385 at 20iterations 1.120976 36.28699 at 30iterations 0.5486225 16.38799 at 40iterations 0.2690603 8.452930 at 50iterations 0.1320580 4.141756 at 60iterations 6.4955615E-02 1.835363 at 70iterations 3.1940077E-02 1.168840 at 80iterations 1.5879039E-02 0.4455051 at 90iterations 7.9921372E-03 0.2354965 at 100iterations 4.1060480E-03 0.1239719 at 110iterations 2.1930952E-03 6.9824219E-02 at 120iterations finished qdiffx linear iterations at : 13:02:43 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.1930952E-03 6.9824219E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 13:02:44 7.933u 0.216s 0:08.46 96.2% 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 Sun Oct 9 2011 at 13:02:44 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2357 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.072910 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): -6.854000 44.44300 ymin,ymax (A): -14.17700 37.95600 zmin,zma (A): 2.782000 45.08500 x,y,z range (A): 51.29700 52.13300 42.30300 scale (grids/A): 3.072910 object centre (A): 18.79450 11.88950 23.93350 number of atom coordinates read : 2357 total number of charged atoms : 2212 net assigned charge : 4.406012 assigned positive charge : 359.9892 centred at (gu) : 88.62852 93.77920 92.35812 assigned negative charge : -355.5836 centred at (gu) : 88.64005 94.29382 92.58400 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21353 grid for indexing accessible points = 1.400000 m= 98272 mr = 132981 m= 39045 mr = 80573 m= 10497 mr = 31879 m= 1983 mr = 7938 m= 168 mr = 1462 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2757 time to turn everything in is 1.040000 number of dielectric boundary points 78798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 17690 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) : 2.048607 object centre at (A) : 18.79450 11.88950 23.93350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3979824 -1.2796376E-02 midg,1,midg; midg,igrid,midg 0.3062398 -0.4253906 1,midg,midg; igrid,midg,midg 0.4706922 -0.1099203 gauss-seidel spectral radius is 0.9992906 estimated iterations to convergence 296 setup time was (sec) 1.280000 now iterating at: 13:02:45 rms-change max change #iterations 10.64567 415.4104 at 10iterations 6.296511 126.8191 at 20iterations 3.710103 68.72906 at 30iterations 2.184675 43.12967 at 40iterations 1.281507 24.88570 at 50iterations 0.7510552 15.24774 at 60iterations 0.4395487 7.582726 at 70iterations 0.2575225 4.541309 at 80iterations 0.1504072 2.538767 at 90iterations 8.8061608E-02 1.663330 at 100iterations 5.1605836E-02 0.8692780 at 110iterations 3.0428605E-02 0.5063877 at 120iterations 1.8056750E-02 0.3220005 at 130iterations 1.0948432E-02 0.2315292 at 140iterations 6.8550585E-03 0.1455650 at 150iterations 4.4943308E-03 9.6702576E-02 at 160iterations 3.1415371E-03 7.2845459E-02 at 170iterations 2.3362085E-03 5.0230026E-02 at 180iterations finished qdiffx linear iterations at : 13:02:56 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 2.3362085E-03 5.0230026E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 13:02:57 12.695u 0.218s 0:13.18 97.8% 0+0k 0+0io 0pf+0w