Mon Oct 10 17:00:42 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 Mon Oct 10 2011 at 17:00:42 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: ZN8 819 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5130422 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): -15.07800 36.24000 ymin,ymax (A): -30.49400 31.45600 zmin,zma (A): -3.748000 65.64200 x,y,z range (A): 51.31800 61.95000 69.39000 scale (grids/A): 0.5130422 object centre (A): 10.58100 0.4809999 30.94700 number of atom coordinates read : 4218 total number of charged atoms : 4016 net assigned charge : 0.3000247 assigned positive charge : 628.7874 centred at (gu) : 90.39650 90.59401 87.51283 assigned negative charge : -628.4913 centred at (gu) : 90.26701 90.60746 87.60773 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6994 nv = 96 ne = 84 npr = 86011 no. pairs analyzed = 86011 no. exposed pairs = 5494 no. arc points = 37989 no. surface atoms = 1834 nbur = 2384 mkacc time = 0.1500000 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 = 1.652000 m= 266 mr = 3553 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3654 ## 518 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9353 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5547838E-10 -1.2708129E-10 midg,1,midg; midg,igrid,midg 2.6390163E-11 -4.3090417E-11 1,midg,midg; igrid,midg,midg -3.0047947E-10 3.5229705E-10 gauss-seidel spectral radius is 0.9805306 estimated iterations to convergence 59 setup time was (sec) 0.4700000 now iterating at: 17:00:42 rms-change max change #iterations 6.5765657E-02 15.91498 at 10iterations 3.6940500E-03 0.5601730 at 20iterations 3.0792839E-04 5.4779053E-02 at 30iterations 7.5075295E-05 1.1426687E-02 at 40iterations 2.5596080E-05 3.8679838E-03 at 50iterations finished qdiffx linear iterations at : 17:00:45 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.5596080E-05 3.8679838E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:00:46 3.488u 0.195s 0:04.11 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 17:00:46 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: ZN8 819 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.539127 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): -15.07800 36.24000 ymin,ymax (A): -30.49400 31.45600 zmin,zma (A): -3.748000 65.64200 x,y,z range (A): 51.31800 61.95000 69.39000 scale (grids/A): 1.539127 object centre (A): 10.58100 0.4809999 30.94700 number of atom coordinates read : 4218 total number of charged atoms : 4016 net assigned charge : 0.3000247 assigned positive charge : 628.7874 centred at (gu) : 91.18880 91.78073 82.53729 assigned negative charge : -628.4913 centred at (gu) : 90.80064 91.82207 82.82301 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22809 mr = 53056 m= 1991 mr = 14932 m= 39 mr = 835 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3800000 number of dielectric boundary points 34718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 30182 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) : 0.5130422 object centre at (A) : 10.58100 0.4809999 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1714312E-03 -1.2515529E-02 midg,1,midg; midg,igrid,midg -3.5543144E-03 -8.1693744E-03 1,midg,midg; igrid,midg,midg -1.2180114E-03 8.4256670E-03 gauss-seidel spectral radius is 0.9980786 estimated iterations to convergence 181 setup time was (sec) 0.6000000 now iterating at: 17:00:47 rms-change max change #iterations 3.556854 153.9808 at 10iterations 1.445280 51.98959 at 20iterations 0.5840527 20.88507 at 30iterations 0.2374783 7.939148 at 40iterations 9.6869715E-02 3.760500 at 50iterations 3.9512802E-02 1.339864 at 60iterations 1.6027730E-02 0.5394497 at 70iterations 6.5501807E-03 0.2149363 at 80iterations 2.6682620E-03 0.1028404 at 90iterations 1.0893553E-03 3.5034180E-02 at 100iterations 4.4909064E-04 1.4789581E-02 at 110iterations 1.8815231E-04 6.7901611E-03 at 120iterations finished qdiffx linear iterations at : 17:00:54 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.8815231E-04 6.7901611E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 17:00:54 7.868u 0.220s 0:08.69 92.9% 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 17:00:54 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: ZN8 819 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.308690 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): -15.07800 36.24000 ymin,ymax (A): -30.49400 31.45600 zmin,zma (A): -3.748000 65.64200 x,y,z range (A): 51.31800 61.95000 69.39000 scale (grids/A): 2.308690 object centre (A): 10.58100 0.4809999 30.94700 number of atom coordinates read : 4218 total number of charged atoms : 4016 net assigned charge : 0.3000247 assigned positive charge : 628.7874 centred at (gu) : 91.78271 92.67074 78.80596 assigned negative charge : -628.4913 centred at (gu) : 91.20094 92.73308 79.23447 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 183322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81130 mr = 130574 m= 20407 mr = 62702 m= 2820 mr = 14447 m= 140 mr = 1657 m= 0 mr = 42 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 210 time to turn everything in is 0.9400000 number of dielectric boundary points 78397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 32056 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) : 1.539127 object centre at (A) : 10.58100 0.4809999 30.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1433735 -0.2797458 midg,1,midg; midg,igrid,midg -0.1358968 -0.1908331 1,midg,midg; igrid,midg,midg -6.6771866E-03 0.1296749 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 1.180000 now iterating at: 17:00:56 rms-change max change #iterations 9.688092 282.9979 at 10iterations 5.554955 173.7233 at 20iterations 3.137161 74.98230 at 30iterations 1.773067 39.21254 at 40iterations 0.9935286 25.78015 at 50iterations 0.5549628 12.77793 at 60iterations 0.3089086 7.391876 at 70iterations 0.1717137 4.348770 at 80iterations 9.5197856E-02 2.174095 at 90iterations 5.2741878E-02 1.023047 at 100iterations 2.9232662E-02 0.6384888 at 110iterations 1.6136670E-02 0.3319016 at 120iterations 8.9252945E-03 0.1780052 at 130iterations 4.9172118E-03 0.1154480 at 140iterations 2.7107922E-03 5.5345535E-02 at 150iterations 1.5016141E-03 3.0377865E-02 at 160iterations 8.2906563E-04 1.5310645E-02 at 170iterations 4.5701195E-04 9.6817017E-03 at 180iterations finished qdiffx linear iterations at : 17:01:07 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 4.5701195E-04 9.6817017E-03 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 17:01:09 12.906u 0.213s 0:14.16 92.5% 0+0k 0+0io 0pf+0w