Mon Oct 10 14:00:29 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 Mon Oct 10 2011 at 14:00:30 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: NAP 207 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7187853 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 0.7187853 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2081 net assigned charge : 5.525020 assigned positive charge : 334.8285 centred at (gu) : 90.00447 90.59477 90.62472 assigned negative charge : -329.3039 centred at (gu) : 89.92966 90.68351 90.75693 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7660 nv = 96 ne = 84 npr = 45958 no. pairs analyzed = 45958 no. exposed pairs = 2779 no. arc points = 19585 no. surface atoms = 932 nbur = 1288 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4217 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.2900000 number of dielectric boundary points 3838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1734 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8498 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3233490E-07 -3.2011371E-08 midg,1,midg; midg,igrid,midg 1.0775896E-07 1.6490236E-09 1,midg,midg; igrid,midg,midg 1.1364090E-08 1.1159641E-07 gauss-seidel spectral radius is 0.9899255 estimated iterations to convergence 81 setup time was (sec) 0.5200000 now iterating at: 14:00:30 rms-change max change #iterations 0.2256020 29.93509 at 10iterations 2.8662236E-02 3.921963 at 20iterations 3.5847966E-03 0.4709358 at 30iterations 4.6178518E-04 5.3352356E-02 at 40iterations 5.9208556E-05 7.9913139E-03 at 50iterations finished qdiffx linear iterations at : 14:00:33 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.9208556E-05 7.9913139E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:00:34 3.402u 0.157s 0:04.34 81.7% 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 Mon Oct 10 2011 at 14:00:34 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: NAP 207 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.156356 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 2.156356 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2081 net assigned charge : 5.525020 assigned positive charge : 334.8285 centred at (gu) : 90.01314 91.78400 91.87377 assigned negative charge : -329.3039 centred at (gu) : 89.78886 92.05051 92.27076 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19585 grid for indexing accessible points = 1.400000 m= 31114 mr = 55703 m= 6467 mr = 23484 m= 686 mr = 4403 m= 35 mr = 381 m= 0 mr = 9 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1107 time to turn everything in is 0.6600000 number of dielectric boundary points 35267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 16553 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) : 0.7187853 object centre at (A) : 43.74950 0.5100002 15.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6731198E-02 5.4293443E-03 midg,1,midg; midg,igrid,midg 3.7632387E-02 3.2930043E-02 1,midg,midg; igrid,midg,midg -1.2908653E-02 3.6214404E-02 gauss-seidel spectral radius is 0.9988782 estimated iterations to convergence 236 setup time was (sec) 0.9400000 now iterating at: 14:00:35 rms-change max change #iterations 4.948594 177.3351 at 10iterations 2.492137 86.20326 at 20iterations 1.249220 40.69031 at 30iterations 0.6274246 19.08381 at 40iterations 0.3150441 9.616673 at 50iterations 0.1575941 4.371991 at 60iterations 7.9410128E-02 2.368450 at 70iterations 4.0015657E-02 1.144348 at 80iterations 2.0115862E-02 0.6543941 at 90iterations 1.0077511E-02 0.3124180 at 100iterations 5.0676563E-03 0.1400948 at 110iterations 2.5462317E-03 6.9252014E-02 at 120iterations finished qdiffx linear iterations at : 14:00:42 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 2.5462317E-03 6.9252014E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 14:00:43 7.793u 0.181s 0:09.48 84.0% 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 Mon Oct 10 2011 at 14:00:43 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: NAP 207 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: 3.234534 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): 20.50500 66.99400 ymin,ymax (A): -24.25400 25.27400 zmin,zma (A): -4.401000 34.87600 x,y,z range (A): 46.48900 49.52800 39.27700 scale (grids/A): 3.234534 object centre (A): 43.74950 0.5100002 15.23750 number of atom coordinates read : 2220 total number of charged atoms : 2081 net assigned charge : 5.525020 assigned positive charge : 334.8285 centred at (gu) : 90.01955 92.67586 92.81062 assigned negative charge : -329.3039 centred at (gu) : 89.68320 93.07593 93.40621 start vw surface at 0.1600000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 186626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19585 grid for indexing accessible points = 1.400000 m= 96611 mr = 134612 m= 39938 mr = 79491 m= 12277 mr = 33123 m= 2648 mr = 9597 m= 425 mr = 1956 m= 59 mr = 316 m= 0 mr = 44 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3596 time to turn everything in is 2.000000 number of dielectric boundary points 79445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 16648 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) : 2.156356 object centre at (A) : 43.74950 0.5100002 15.23750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7036955 1.0906254E-02 midg,1,midg; midg,igrid,midg 0.2553123 0.4784899 1,midg,midg; igrid,midg,midg -5.9624795E-02 0.2383996 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.300000 now iterating at: 14:00:46 rms-change max change #iterations 10.79782 352.0164 at 10iterations 6.293047 130.3771 at 20iterations 3.666822 65.68205 at 30iterations 2.141258 37.94494 at 40iterations 1.250893 21.51963 at 50iterations 0.7300302 13.11167 at 60iterations 0.4250380 6.878613 at 70iterations 0.2475692 4.169362 at 80iterations 0.1442340 2.484230 at 90iterations 8.4028892E-02 1.402262 at 100iterations 4.9014099E-02 0.8326542 at 110iterations 2.8536370E-02 0.5354919 at 120iterations 1.6632080E-02 0.2731241 at 130iterations 9.6781077E-03 0.1544094 at 140iterations 5.6617758E-03 9.5596313E-02 at 150iterations 3.2993844E-03 5.0884247E-02 at 160iterations 1.9211707E-03 3.2413483E-02 at 170iterations 1.1217392E-03 1.9386292E-02 at 180iterations finished qdiffx linear iterations at : 14:00:57 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 1.1217392E-03 1.9386292E-02 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 14:00:59 13.860u 0.218s 0:15.12 93.0% 0+0k 0+0io 0pf+0w