Mon Oct 10 14:04:13 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 14:04:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: ASL 42 has a net charge of -0.1000 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: 0.7032515 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 0.7032515 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -10.09998 assigned positive charge : 333.9758 centred at (gu) : 88.47914 88.37640 90.09173 assigned negative charge : -344.0759 centred at (gu) : 88.40094 88.15432 89.81885 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 45182 no. pairs analyzed = 45182 no. exposed pairs = 2815 no. arc points = 20278 no. surface atoms = 941 nbur = 1258 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4001 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.1900000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1811 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0847133E-07 5.8268739E-08 midg,1,midg; midg,igrid,midg -2.5644232E-07 2.3071362E-08 1,midg,midg; igrid,midg,midg -1.5158940E-07 -2.7322242E-08 gauss-seidel spectral radius is 0.9894814 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 14:04:14 rms-change max change #iterations 0.2079531 31.58620 at 10iterations 2.5152402E-02 3.237354 at 20iterations 3.0175855E-03 0.4194059 at 30iterations 3.6792035E-04 4.8965454E-02 at 40iterations 4.4506178E-05 5.6219101E-03 at 50iterations finished qdiffx linear iterations at : 14:04:16 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.4506178E-05 5.6219101E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:04:17 3.402u 0.213s 0:04.10 88.0% 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 14:04:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: ASL 42 has a net charge of -0.1000 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: 2.109755 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 2.109755 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -10.09998 assigned positive charge : 333.9758 centred at (gu) : 85.43722 85.12892 90.27488 assigned negative charge : -344.0759 centred at (gu) : 85.20262 84.46300 89.45645 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 29502 mr = 53006 m= 5381 mr = 22080 m= 432 mr = 3590 m= 12 mr = 220 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3167 time to turn everything in is 0.4000000 number of dielectric boundary points 34668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16332 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) : 0.7032515 object centre at (A) : 15.51550 5.947001 47.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1167118 -1.1866035E-02 midg,1,midg; midg,igrid,midg -0.1137930 1.1329374E-02 1,midg,midg; igrid,midg,midg -1.8377472E-02 1.5327785E-03 gauss-seidel spectral radius is 0.9988384 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 14:04:18 rms-change max change #iterations 4.844722 187.9921 at 10iterations 2.392341 79.59142 at 20iterations 1.183272 37.66512 at 30iterations 0.5864652 17.75385 at 40iterations 0.2914035 9.454330 at 50iterations 0.1443488 4.238937 at 60iterations 7.1453229E-02 2.196953 at 70iterations 3.5472810E-02 1.049282 at 80iterations 1.7610779E-02 0.5245857 at 90iterations 8.7259412E-03 0.2625504 at 100iterations 4.3482101E-03 0.1311989 at 110iterations 2.1571615E-03 6.8827748E-02 at 120iterations finished qdiffx linear iterations at : 14:04:25 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.1571615E-03 6.8827748E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 14:04:26 8.024u 0.254s 0:08.88 93.1% 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 14:04:26 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: ASL 42 has a net charge of -0.1000 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: 3.164632 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 3.164632 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -10.09998 assigned positive charge : 333.9758 centred at (gu) : 83.15584 82.69347 90.41225 assigned negative charge : -344.0759 centred at (gu) : 82.80396 81.69443 89.18466 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 92231 mr = 128222 m= 36329 mr = 75596 m= 10092 mr = 29830 m= 1887 mr = 7917 m= 184 mr = 1387 m= 5 mr = 91 m= 0 mr = 2 time to grow re-entrant surface = 0.6000001 no. cavity mid-points inaccessible to solvent = 10358 time to turn everything in is 1.220000 number of dielectric boundary points 78125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16448 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) : 2.109755 object centre at (A) : 15.51550 5.947001 47.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.120051 -4.2008776E-02 midg,1,midg; midg,igrid,midg -0.9335952 6.9690913E-02 1,midg,midg; igrid,midg,midg -6.7815565E-02 1.9848213E-02 gauss-seidel spectral radius is 0.9993040 estimated iterations to convergence 299 setup time was (sec) 1.470000 now iterating at: 14:04:28 rms-change max change #iterations 10.88596 385.1675 at 10iterations 6.406232 126.6707 at 20iterations 3.755631 69.83612 at 30iterations 2.203534 39.33128 at 40iterations 1.287833 23.59995 at 50iterations 0.7538092 12.28670 at 60iterations 0.4403795 8.633354 at 70iterations 0.2570168 4.637943 at 80iterations 0.1504101 2.443155 at 90iterations 8.7781988E-02 1.606371 at 100iterations 5.1176511E-02 0.8979836 at 110iterations 2.9940801E-02 0.5143051 at 120iterations 1.7446330E-02 0.3050804 at 130iterations 1.0196238E-02 0.1675582 at 140iterations 5.9607280E-03 0.1006136 at 150iterations 3.4740858E-03 5.9990406E-02 at 160iterations 2.0300529E-03 3.5289764E-02 at 170iterations 1.1863830E-03 2.0644188E-02 at 180iterations finished qdiffx linear iterations at : 14:04:40 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 1.1863830E-03 2.0644188E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 14:04:40 13.271u 0.550s 0:14.35 96.3% 0+0k 0+0io 0pf+0w