Sat Oct 8 18:28:14 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+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 Sat Oct 8 2011 at 18:28:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 0.6284534 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 0.6284534 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 396.4450 centred at (gu) : 88.47085 89.49511 89.89146 assigned negative charge : -391.9455 centred at (gu) : 88.36681 89.53365 89.77743 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 53678 no. pairs analyzed = 53678 no. exposed pairs = 3077 no. arc points = 21703 no. surface atoms = 1035 nbur = 1568 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3857 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.1900000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2103 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1564570E-09 1.4084470E-08 midg,1,midg; midg,igrid,midg 9.0231875E-09 1.3840772E-09 1,midg,midg; igrid,midg,midg -5.9754166E-09 9.7716732E-09 gauss-seidel spectral radius is 0.9868826 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 18:28:15 rms-change max change #iterations 0.1357675 24.40591 at 10iterations 1.2839331E-02 1.840363 at 20iterations 1.2330092E-03 0.1760845 at 30iterations 1.1771371E-04 1.6971588E-02 at 40iterations 1.1267107E-05 1.4533997E-03 at 50iterations finished qdiffx linear iterations at : 18:28:18 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1267107E-05 1.4533997E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 18:28:18 3.410u 0.165s 0:03.85 92.7% 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 Sat Oct 8 2011 at 18:28:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 1.885360 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 1.885360 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 396.4450 centred at (gu) : 85.41203 88.48507 89.67384 assigned negative charge : -391.9455 centred at (gu) : 85.10015 88.60073 89.33199 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 26537 mr = 51771 m= 3861 mr = 19864 m= 230 mr = 2445 m= 1 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4367 time to turn everything in is 0.3600000 number of dielectric boundary points 30136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19532 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) : 0.6284534 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0544570E-02 3.4603149E-02 midg,1,midg; midg,igrid,midg 1.3030975E-02 -8.9555752E-04 1,midg,midg; igrid,midg,midg -3.3040443E-03 3.8769461E-02 gauss-seidel spectral radius is 0.9986049 estimated iterations to convergence 212 setup time was (sec) 0.5700000 now iterating at: 18:28:19 rms-change max change #iterations 4.143242 179.8076 at 10iterations 1.925137 61.37941 at 20iterations 0.8958786 28.46332 at 30iterations 0.4158744 14.77536 at 40iterations 0.1928265 5.987643 at 50iterations 8.9896478E-02 2.852604 at 60iterations 4.1681036E-02 1.321409 at 70iterations 1.9416526E-02 0.6269748 at 80iterations 9.0210102E-03 0.3021002 at 90iterations 4.2027752E-03 0.1331005 at 100iterations 1.9522287E-03 6.1080933E-02 at 110iterations 9.0697856E-04 2.7488708E-02 at 120iterations finished qdiffx linear iterations at : 18:28:26 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 9.0697856E-04 2.7488708E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 18:28:27 7.806u 0.200s 0:08.27 96.7% 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 Sat Oct 8 2011 at 18:28:27 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 501 has a net charge of 1.4000 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: 2.828040 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 2.828040 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2603 total number of charged atoms : 2487 net assigned charge : 4.500006 assigned positive charge : 396.4450 centred at (gu) : 83.11790 87.72761 89.51054 assigned negative charge : -391.9455 centred at (gu) : 82.65015 87.90099 88.99790 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 86699 mr = 124734 m= 30685 mr = 71795 m= 6893 mr = 25020 m= 972 mr = 5319 m= 58 mr = 703 m= 0 mr = 20 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 14265 time to turn everything in is 0.9200000 number of dielectric boundary points 67870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19894 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) : 1.885360 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1464556 0.3870697 midg,1,midg; midg,igrid,midg 0.1563577 -3.9897881E-02 1,midg,midg; igrid,midg,midg 5.0227423E-03 0.4814594 gauss-seidel spectral radius is 0.9992449 estimated iterations to convergence 287 setup time was (sec) 1.160000 now iterating at: 18:28:28 rms-change max change #iterations 9.711741 334.6756 at 10iterations 5.594885 153.8988 at 20iterations 3.198706 66.50674 at 30iterations 1.831435 34.25503 at 40iterations 1.049297 19.09439 at 50iterations 0.5984566 12.40469 at 60iterations 0.3426861 6.551407 at 70iterations 0.1956047 3.493866 at 80iterations 0.1118092 1.977018 at 90iterations 6.3630164E-02 1.211607 at 100iterations 3.6401164E-02 0.6978207 at 110iterations 2.0734040E-02 0.3670731 at 120iterations 1.1881266E-02 0.2168980 at 130iterations 6.7731966E-03 0.1241875 at 140iterations 3.8668495E-03 6.9114685E-02 at 150iterations 2.2086506E-03 3.8314819E-02 at 160iterations 1.2583996E-03 2.3696899E-02 at 170iterations 7.2025869E-04 1.2513161E-02 at 180iterations finished qdiffx linear iterations at : 18:28:39 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 7.2025869E-04 1.2513161E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 18:28:40 12.593u 0.220s 0:13.09 97.8% 0+0k 0+0io 0pf+0w