Mon Oct 10 14:15:48 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 14:15:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5988528 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): -7.960000 51.48700 ymin,ymax (A): -15.91600 33.97700 zmin,zma (A): 77.26100 130.2700 x,y,z range (A): 59.44700 49.89300 53.00900 scale (grids/A): 0.5988528 object centre (A): 21.76350 9.030499 103.7655 number of atom coordinates read : 2743 total number of charged atoms : 2600 net assigned charge : -4.099987 assigned positive charge : 427.6484 centred at (gu) : 91.79768 89.54794 89.60812 assigned negative charge : -431.7493 centred at (gu) : 91.73525 89.63391 89.66360 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6613 nv = 96 ne = 84 npr = 53888 no. pairs analyzed = 53888 no. exposed pairs = 3810 no. arc points = 26434 no. surface atoms = 1280 nbur = 1463 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 333 mr = 3296 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2653 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8135 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3944504E-10 -3.6044410E-09 midg,1,midg; midg,igrid,midg 1.7477706E-09 -4.6459103E-09 1,midg,midg; igrid,midg,midg -2.8140326E-09 1.0619100E-09 gauss-seidel spectral radius is 0.9855869 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 14:15:49 rms-change max change #iterations 0.1162541 17.80864 at 10iterations 9.7548896E-03 1.585316 at 20iterations 8.5883972E-04 0.1376953 at 30iterations 1.0540163E-04 1.5907288E-02 at 40iterations 2.4809202E-05 3.7622452E-03 at 50iterations finished qdiffx linear iterations at : 14:15:53 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 2.4809202E-05 3.7622452E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 14:15:54 4.438u 0.412s 0:05.42 89.2% 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 Mon Oct 10 2011 at 14:15:54 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.796558 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): -7.960000 51.48700 ymin,ymax (A): -15.91600 33.97700 zmin,zma (A): 77.26100 130.2700 x,y,z range (A): 59.44700 49.89300 53.00900 scale (grids/A): 1.796558 object centre (A): 21.76350 9.030499 103.7655 number of atom coordinates read : 2743 total number of charged atoms : 2600 net assigned charge : -4.099987 assigned positive charge : 427.6484 centred at (gu) : 95.39220 88.64314 88.82356 assigned negative charge : -431.7493 centred at (gu) : 95.20526 88.90135 88.99043 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26434 grid for indexing accessible points = 1.400000 m= 24524 mr = 47042 m= 3412 mr = 16681 m= 133 mr = 1815 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20218 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) : 0.5988528 object centre at (A) : 21.76350 9.030499 103.7655 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3545811E-02 -3.3974268E-02 midg,1,midg; midg,igrid,midg -4.5071323E-03 -2.0518566E-02 1,midg,midg; igrid,midg,midg 2.0184705E-02 3.2907531E-02 gauss-seidel spectral radius is 0.9984956 estimated iterations to convergence 204 setup time was (sec) 0.9400000 now iterating at: 14:15:55 rms-change max change #iterations 4.049274 175.7075 at 10iterations 1.822298 64.30978 at 20iterations 0.8182524 30.01875 at 30iterations 0.3701937 14.58938 at 40iterations 0.1669243 6.882767 at 50iterations 7.5169332E-02 2.646534 at 60iterations 3.3878464E-02 1.082119 at 70iterations 1.5301172E-02 0.5280247 at 80iterations 6.9329669E-03 0.2143250 at 90iterations 3.1424458E-03 0.1117296 at 100iterations 1.4394156E-03 4.7688484E-02 at 110iterations 6.6510733E-04 2.1549225E-02 at 120iterations finished qdiffx linear iterations at : 14:16:05 total time elapsed so far: 10.58000 # loops : 120 mean,max change (kT/e) : 6.6510733E-04 2.1549225E-02 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 14:16:06 10.748u 0.445s 0:11.88 94.1% 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 14:16:06 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: ADP 661 has a net charge of -2.0000 !!! WARNING: MG6 663 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.694837 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): -7.960000 51.48700 ymin,ymax (A): -15.91600 33.97700 zmin,zma (A): 77.26100 130.2700 x,y,z range (A): 59.44700 49.89300 53.00900 scale (grids/A): 2.694837 object centre (A): 21.76350 9.030499 103.7655 number of atom coordinates read : 2743 total number of charged atoms : 2600 net assigned charge : -4.099987 assigned positive charge : 427.6484 centred at (gu) : 98.08813 87.96461 88.23525 assigned negative charge : -431.7493 centred at (gu) : 97.80779 88.35201 88.48551 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 164341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26434 grid for indexing accessible points = 1.400000 m= 79824 mr = 115007 m= 27159 mr = 62443 m= 5674 mr = 20527 m= 603 mr = 3780 m= 14 mr = 316 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 75542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 20798 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) : 1.796558 object centre at (A) : 21.76350 9.030499 103.7655 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1362661 -0.4465590 midg,1,midg; midg,igrid,midg -7.7734411E-02 -0.1997970 1,midg,midg; igrid,midg,midg 0.4395376 0.3295859 gauss-seidel spectral radius is 0.9992291 estimated iterations to convergence 284 setup time was (sec) 1.920000 now iterating at: 14:16:08 rms-change max change #iterations 9.988882 291.9601 at 10iterations 5.824256 142.4059 at 20iterations 3.366466 73.29224 at 30iterations 1.942208 44.33900 at 40iterations 1.111870 23.43678 at 50iterations 0.6377288 13.25421 at 60iterations 0.3641326 7.432392 at 70iterations 0.2083031 4.307327 at 80iterations 0.1186735 2.383207 at 90iterations 6.7590371E-02 1.332727 at 100iterations 3.8440585E-02 0.8014297 at 110iterations 2.1866072E-02 0.4092063 at 120iterations 1.2461287E-02 0.2381783 at 130iterations 7.0984913E-03 0.1415977 at 140iterations 4.0561338E-03 8.3343506E-02 at 150iterations 2.3311258E-03 5.1422119E-02 at 160iterations 1.3440053E-03 2.3714304E-02 at 170iterations 7.9224433E-04 1.4949799E-02 at 180iterations finished qdiffx linear iterations at : 14:16:24 total time elapsed so far: 17.87000 # loops : 180 mean,max change (kT/e) : 7.9224433E-04 1.4949799E-02 energy calculations done at 17.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.04000 DelPhi exited at 14:16:25 18.042u 0.453s 0:18.87 97.9% 0+0k 0+0io 0pf+0w