Tue Oct 11 03:43:52 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 Tue Oct 11 2011 at 03:43:52 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6360778 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 0.6360778 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2650 net assigned charge : 2.162019 assigned positive charge : 424.4916 centred at (gu) : 89.89684 90.13097 91.93040 assigned negative charge : -422.3302 centred at (gu) : 89.66830 90.02528 91.89668 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7370 nv = 96 ne = 84 npr = 56738 no. pairs analyzed = 56738 no. exposed pairs = 3344 no. arc points = 23205 no. surface atoms = 1125 nbur = 1656 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 4142 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2324 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6526595E-10 1.0011686E-08 midg,1,midg; midg,igrid,midg -9.1041787E-09 1.5056276E-08 1,midg,midg; igrid,midg,midg -2.4398370E-08 2.7459322E-08 gauss-seidel spectral radius is 0.9872047 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 03:43:53 rms-change max change #iterations 0.1452625 20.73884 at 10iterations 1.4281183E-02 2.043709 at 20iterations 1.4466161E-03 0.2093210 at 30iterations 1.5095195E-04 2.2380829E-02 at 40iterations 1.6815542E-05 2.2392273E-03 at 50iterations finished qdiffx linear iterations at : 03:43:56 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.6815542E-05 2.2392273E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 03:43:57 3.625u 0.225s 0:04.58 83.8% 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 03:43:57 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.908233 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 1.908233 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2650 net assigned charge : 2.162019 assigned positive charge : 424.4916 centred at (gu) : 89.69002 90.39233 95.79046 assigned negative charge : -422.3302 centred at (gu) : 89.00491 90.07559 95.68980 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 28629 mr = 56333 m= 4327 mr = 21188 m= 226 mr = 2692 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.6100000 number of dielectric boundary points 32668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20813 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) : 0.6360778 object centre at (A) : 13.05800 -1.879499 17.25000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1999605E-02 7.2709280E-03 midg,1,midg; midg,igrid,midg -1.4296045E-02 -4.4699251E-03 1,midg,midg; igrid,midg,midg -1.0084131E-02 5.0786451E-02 gauss-seidel spectral radius is 0.9986539 estimated iterations to convergence 216 setup time was (sec) 0.9200000 now iterating at: 03:43:58 rms-change max change #iterations 4.466518 206.6655 at 10iterations 2.105016 74.01394 at 20iterations 0.9941239 33.07386 at 30iterations 0.4705144 15.38080 at 40iterations 0.2212755 6.580791 at 50iterations 0.1042965 3.326807 at 60iterations 4.9396634E-02 1.506724 at 70iterations 2.3306325E-02 0.7064514 at 80iterations 1.0997792E-02 0.3261776 at 90iterations 5.1845661E-03 0.1624222 at 100iterations 2.4442733E-03 7.3299408E-02 at 110iterations 1.1599164E-03 3.5395145E-02 at 120iterations finished qdiffx linear iterations at : 03:44:05 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.1599164E-03 3.5395145E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 03:44:06 8.032u 0.221s 0:08.64 95.4% 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 03:44:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.862350 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): -11.04400 37.16000 ymin,ymax (A): -26.96700 23.20800 zmin,zma (A): -10.73400 45.23400 x,y,z range (A): 48.20400 50.17500 55.96800 scale (grids/A): 2.862350 object centre (A): 13.05800 -1.879499 17.25000 number of atom coordinates read : 2781 total number of charged atoms : 2650 net assigned charge : 2.162019 assigned positive charge : 424.4916 centred at (gu) : 89.53503 90.58824 98.68544 assigned negative charge : -422.3302 centred at (gu) : 88.50725 90.11329 98.53458 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 184741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 93395 mr = 136513 m= 32754 mr = 76606 m= 7584 mr = 26324 m= 1027 mr = 5735 m= 63 mr = 702 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1367 time to turn everything in is 1.540000 number of dielectric boundary points 73649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 21182 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) : 1.908233 object centre at (A) : 13.05800 -1.879499 17.25000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4986860 0.2582132 midg,1,midg; midg,igrid,midg -0.1862139 -0.1373347 1,midg,midg; igrid,midg,midg -4.2157277E-02 0.4629846 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 1.880000 now iterating at: 03:44:08 rms-change max change #iterations 10.38313 420.3739 at 10iterations 6.063329 178.4149 at 20iterations 3.528205 77.83284 at 30iterations 2.040132 41.62985 at 40iterations 1.184608 26.21993 at 50iterations 0.6834694 13.42791 at 60iterations 0.3951033 7.622025 at 70iterations 0.2279499 3.986997 at 80iterations 0.1317495 2.356299 at 90iterations 7.5982064E-02 1.456699 at 100iterations 4.3888822E-02 0.7526722 at 110iterations 2.5242275E-02 0.4474721 at 120iterations 1.4569595E-02 0.2732430 at 130iterations 8.4058754E-03 0.1429157 at 140iterations 4.8553590E-03 8.6383700E-02 at 150iterations 2.8118568E-03 5.4187775E-02 at 160iterations 1.6327404E-03 2.9571533E-02 at 170iterations 9.5414411E-04 1.6204834E-02 at 180iterations finished qdiffx linear iterations at : 03:44:19 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 9.5414411E-04 1.6204834E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 03:44:19 13.132u 0.234s 0:13.76 97.0% 0+0k 0+0io 0pf+0w