Tue Oct 11 07:51:06 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 07:51:06 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6366693 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 0.6366693 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2414 net assigned charge : 9.039014 assigned positive charge : 391.1410 centred at (gu) : 90.23634 87.03497 90.84486 assigned negative charge : -382.1027 centred at (gu) : 90.25698 86.99918 91.04108 start vw surface at 0.2400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 6761 nv = 96 ne = 84 npr = 51562 no. pairs analyzed = 51562 no. exposed pairs = 3018 no. arc points = 21065 no. surface atoms = 1022 nbur = 1759 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3835 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.4000000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2027 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8162 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6775650E-08 -1.0511329E-08 midg,1,midg; midg,igrid,midg 1.5567768E-08 8.5946370E-09 1,midg,midg; igrid,midg,midg 1.3615150E-08 1.0527764E-08 gauss-seidel spectral radius is 0.9872097 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 07:51:07 rms-change max change #iterations 0.1407579 20.96516 at 10iterations 1.4289618E-02 1.984608 at 20iterations 1.7817672E-03 0.2924194 at 30iterations 2.9435646E-04 4.2167664E-02 at 40iterations 6.3279287E-05 1.0055542E-02 at 50iterations finished qdiffx linear iterations at : 07:51:10 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 6.3279287E-05 1.0055542E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 07:51:10 3.271u 0.185s 0:03.85 89.6% 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 07:51:10 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.910008 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 1.910008 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2414 net assigned charge : 9.039014 assigned positive charge : 391.1410 centred at (gu) : 90.70871 81.10441 92.53393 assigned negative charge : -382.1027 centred at (gu) : 90.77087 80.99738 93.12281 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21065 grid for indexing accessible points = 1.400000 m= 27466 mr = 52067 m= 4014 mr = 20705 m= 221 mr = 2441 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 603 time to turn everything in is 0.5500000 number of dielectric boundary points 30135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18956 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) : 0.6366693 object centre at (A) : 14.19400 4.473499 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3784970E-02 -1.1365331E-02 midg,1,midg; midg,igrid,midg 1.5101462E-02 2.3684537E-02 1,midg,midg; igrid,midg,midg 1.6763708E-02 2.3006167E-02 gauss-seidel spectral radius is 0.9986266 estimated iterations to convergence 214 setup time was (sec) 0.8100000 now iterating at: 07:51:11 rms-change max change #iterations 4.248742 175.3260 at 10iterations 1.985725 70.69407 at 20iterations 0.9295689 28.79065 at 30iterations 0.4351048 13.17404 at 40iterations 0.2047730 6.535285 at 50iterations 9.5639363E-02 3.151934 at 60iterations 4.4961620E-02 1.374115 at 70iterations 2.1085873E-02 0.6619775 at 80iterations 9.9423369E-03 0.3757005 at 90iterations 4.6979920E-03 0.1740799 at 100iterations 2.2531787E-03 6.9774151E-02 at 110iterations 1.0971098E-03 3.7432671E-02 at 120iterations finished qdiffx linear iterations at : 07:51:18 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.0971098E-03 3.7432671E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 07:51:19 7.904u 0.231s 0:08.64 94.0% 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 Tue Oct 11 2011 at 07:51:19 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.865012 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): -13.76400 42.15200 ymin,ymax (A): -21.79700 30.74400 zmin,zma (A): -11.55100 40.43600 x,y,z range (A): 55.91600 52.54100 51.98700 scale (grids/A): 2.865012 object centre (A): 14.19400 4.473499 14.44250 number of atom coordinates read : 2781 total number of charged atoms : 2414 net assigned charge : 9.039014 assigned positive charge : 391.1410 centred at (gu) : 91.06307 76.65660 93.80090 assigned negative charge : -382.1027 centred at (gu) : 91.15619 76.49606 94.68409 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 170306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21065 grid for indexing accessible points = 1.400000 m= 88853 mr = 125489 m= 32297 mr = 73973 m= 7379 mr = 26171 m= 938 mr = 5381 m= 53 mr = 631 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 2045 time to turn everything in is 1.350000 number of dielectric boundary points 68167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19310 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) : 1.910008 object centre at (A) : 14.19400 4.473499 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7132294 -0.2060943 midg,1,midg; midg,igrid,midg 0.1344367 0.2077194 1,midg,midg; igrid,midg,midg 7.3648088E-02 0.1345744 gauss-seidel spectral radius is 0.9992474 estimated iterations to convergence 288 setup time was (sec) 1.680000 now iterating at: 07:51:21 rms-change max change #iterations 9.849005 418.9800 at 10iterations 5.705167 137.0539 at 20iterations 3.290029 71.29636 at 30iterations 1.892215 37.20545 at 40iterations 1.086601 18.39934 at 50iterations 0.6237997 11.67551 at 60iterations 0.3575675 6.562057 at 70iterations 0.2049686 3.534715 at 80iterations 0.1174265 2.173406 at 90iterations 6.7267150E-02 1.346013 at 100iterations 3.8636163E-02 0.6824303 at 110iterations 2.2201532E-02 0.4015579 at 120iterations 1.2823539E-02 0.2523384 at 130iterations 7.4448436E-03 0.1415253 at 140iterations 4.3670461E-03 7.7865601E-02 at 150iterations 2.6170509E-03 4.9331665E-02 at 160iterations 1.6068732E-03 3.0593872E-02 at 170iterations 1.0300583E-03 1.9729614E-02 at 180iterations finished qdiffx linear iterations at : 07:51:31 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 1.0300583E-03 1.9729614E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 07:51:32 12.224u 0.194s 0:12.80 96.9% 0+0k 0+0io 0pf+0w