Tue Oct 11 02:29:53 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 02:29:53 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6628929 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 0.6628929 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2526 net assigned charge : 4.420027 assigned positive charge : 409.6096 centred at (gu) : 91.21633 90.66798 90.26646 assigned negative charge : -405.1904 centred at (gu) : 91.02115 90.84406 90.32957 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7922 nv = 96 ne = 84 npr = 54504 no. pairs analyzed = 54504 no. exposed pairs = 3254 no. arc points = 22371 no. surface atoms = 1090 nbur = 1575 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 4550 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.2000000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2058 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9244 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4498567E-08 -2.3160247E-09 midg,1,midg; midg,igrid,midg 4.3816542E-08 -3.2249748E-08 1,midg,midg; igrid,midg,midg -2.4866937E-08 7.0283519E-08 gauss-seidel spectral radius is 0.9882103 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 02:29:54 rms-change max change #iterations 0.1788196 21.99207 at 10iterations 1.8894067E-02 2.531948 at 20iterations 2.0496354E-03 0.2989759 at 30iterations 2.2180009E-04 3.1046867E-02 at 40iterations 2.4285393E-05 3.1509399E-03 at 50iterations finished qdiffx linear iterations at : 02:29:57 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.4285393E-05 3.1509399E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 02:29:57 3.349u 0.171s 0:03.93 89.3% 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 02:29:57 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.988679 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 1.988679 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2526 net assigned charge : 4.420027 assigned positive charge : 409.6096 centred at (gu) : 93.64793 92.00334 90.79858 assigned negative charge : -405.1904 centred at (gu) : 93.06319 92.53191 90.98820 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 85689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22371 grid for indexing accessible points = 1.400000 m= 31900 mr = 61053 m= 5429 mr = 24068 m= 399 mr = 3592 m= 8 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4227 time to turn everything in is 0.4000000 number of dielectric boundary points 34536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19941 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) : 0.6628929 object centre at (A) : 43.80500 41.31600 6.319500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2096530E-02 -3.6054943E-02 midg,1,midg; midg,igrid,midg 8.2407981E-02 -1.7667465E-02 1,midg,midg; igrid,midg,midg -1.8687082E-02 5.5801634E-02 gauss-seidel spectral radius is 0.9987512 estimated iterations to convergence 224 setup time was (sec) 0.6100000 now iterating at: 02:29:58 rms-change max change #iterations 4.760505 191.0895 at 10iterations 2.306783 85.63178 at 20iterations 1.112931 35.63708 at 30iterations 0.5397430 16.63153 at 40iterations 0.2613496 7.454865 at 50iterations 0.1263536 4.084266 at 60iterations 6.1370153E-02 1.795088 at 70iterations 2.9711094E-02 0.8766223 at 80iterations 1.4332817E-02 0.4549904 at 90iterations 6.9678784E-03 0.1910191 at 100iterations 3.3770276E-03 9.4106674E-02 at 110iterations 1.6394929E-03 5.0081253E-02 at 120iterations finished qdiffx linear iterations at : 02:30:05 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.6394929E-03 5.0081253E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 02:30:05 7.771u 0.214s 0:08.32 95.9% 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 Tue Oct 11 2011 at 02:30:06 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.983018 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 2.983018 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2526 net assigned charge : 4.420027 assigned positive charge : 409.6096 centred at (gu) : 95.47174 93.00490 91.19759 assigned negative charge : -405.1904 centred at (gu) : 94.59477 93.79782 91.48222 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22371 grid for indexing accessible points = 1.400000 m= 102587 mr = 147538 m= 38450 mr = 85038 m= 10119 mr = 31538 m= 1678 mr = 7917 m= 120 mr = 1154 m= 0 mr = 62 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 14036 time to turn everything in is 1.090000 number of dielectric boundary points 77993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20208 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) : 1.988679 object centre at (A) : 43.80500 41.31600 6.319500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1838441 -0.3922567 midg,1,midg; midg,igrid,midg 1.049299 -0.3846331 1,midg,midg; igrid,midg,midg -0.1876324 0.4563257 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.310000 now iterating at: 02:30:07 rms-change max change #iterations 10.88454 448.0103 at 10iterations 6.357607 155.7675 at 20iterations 3.716863 66.69377 at 30iterations 2.171167 36.66473 at 40iterations 1.264326 22.57424 at 50iterations 0.7345654 13.61603 at 60iterations 0.4278173 7.409838 at 70iterations 0.2486649 4.662278 at 80iterations 0.1445235 2.503611 at 90iterations 8.3895594E-02 1.436882 at 100iterations 4.8785280E-02 0.8038712 at 110iterations 2.8333666E-02 0.4832916 at 120iterations 1.6408008E-02 0.2838593 at 130iterations 9.5266439E-03 0.1667595 at 140iterations 5.5304375E-03 8.8294983E-02 at 150iterations 3.2059841E-03 5.2299500E-02 at 160iterations 1.8633278E-03 3.1967163E-02 at 170iterations 1.0796174E-03 1.7808914E-02 at 180iterations finished qdiffx linear iterations at : 02:30:18 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 1.0796174E-03 1.7808914E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 02:30:19 12.792u 0.219s 0:13.39 97.0% 0+0k 0+0io 0pf+0w