Tue Oct 11 07:58:07 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 07:58:07 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6120519 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 0.6120519 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2338 net assigned charge : 9.519013 assigned positive charge : 382.6272 centred at (gu) : 89.99062 90.08734 89.96519 assigned negative charge : -373.1086 centred at (gu) : 90.05222 90.04279 89.75713 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6033 nv = 96 ne = 84 npr = 50504 no. pairs analyzed = 50504 no. exposed pairs = 2946 no. arc points = 20650 no. surface atoms = 994 nbur = 1489 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 276 mr = 3328 m= 2 mr = 24 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 0.3900000 number of dielectric boundary points 2959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8154325E-09 1.6174118E-08 midg,1,midg; midg,igrid,midg 3.6774259E-09 8.4148928E-09 1,midg,midg; igrid,midg,midg 9.1273096E-09 2.8656042E-09 gauss-seidel spectral radius is 0.9861642 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 07:58:08 rms-change max change #iterations 0.1217498 26.53346 at 10iterations 1.1167193E-02 1.664932 at 20iterations 1.1093691E-03 0.1747589 at 30iterations 1.1839301E-04 2.1102905E-02 at 40iterations 1.4677302E-05 2.4642944E-03 at 50iterations finished qdiffx linear iterations at : 07:58:12 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.4677302E-05 2.4642944E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 07:58:12 4.256u 0.196s 0:04.82 92.1% 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 Tue Oct 11 2011 at 07:58:12 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 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: 1.836156 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 1.836156 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2338 net assigned charge : 9.519013 assigned positive charge : 382.6272 centred at (gu) : 89.97178 90.26189 89.89541 assigned negative charge : -373.1086 centred at (gu) : 90.15632 90.12818 89.27131 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 22454 mr = 46066 m= 2844 mr = 16450 m= 110 mr = 1618 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.6300000 number of dielectric boundary points 27259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 18264 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) : 0.6120519 object centre at (A) : 22.39250 0.2579994 31.52550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7507881E-03 4.1697465E-02 midg,1,midg; midg,igrid,midg 7.7831117E-04 9.0972958E-03 1,midg,midg; igrid,midg,midg 3.1396803E-02 3.5375264E-02 gauss-seidel spectral radius is 0.9985162 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 07:58:13 rms-change max change #iterations 3.890476 184.8710 at 10iterations 1.764791 70.76686 at 20iterations 0.8010707 27.24101 at 30iterations 0.3642024 13.87511 at 40iterations 0.1653986 5.242241 at 50iterations 7.5009003E-02 2.411102 at 60iterations 3.4019124E-02 1.276802 at 70iterations 1.5541566E-02 0.5558922 at 80iterations 7.0362901E-03 0.2595348 at 90iterations 3.2035310E-03 0.1100674 at 100iterations 1.4593692E-03 4.9523354E-02 at 110iterations 6.6280586E-04 2.4085045E-02 at 120iterations finished qdiffx linear iterations at : 07:58:22 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 6.6280586E-04 2.4085045E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 07:58:22 9.610u 0.208s 0:10.10 97.1% 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 Tue Oct 11 2011 at 07:58:22 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 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: 2.754234 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 2.754234 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2338 net assigned charge : 9.519013 assigned positive charge : 382.6272 centred at (gu) : 89.95763 90.39273 89.84306 assigned negative charge : -373.1086 centred at (gu) : 90.23447 90.19230 88.90678 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 152813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 75061 mr = 111477 m= 24307 mr = 61770 m= 4791 mr = 19125 m= 554 mr = 3437 m= 25 mr = 308 m= 0 mr = 13 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1973 time to turn everything in is 1.530000 number of dielectric boundary points 61421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 18696 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) : 1.836156 object centre at (A) : 22.39250 0.2579994 31.52550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1392058 0.4688053 midg,1,midg; midg,igrid,midg -1.0555709E-02 3.5237096E-02 1,midg,midg; igrid,midg,midg 0.1727274 0.1760526 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 1.910000 now iterating at: 07:58:25 rms-change max change #iterations 9.145415 416.8326 at 10iterations 5.223204 124.9529 at 20iterations 2.963971 74.49109 at 30iterations 1.681684 37.42198 at 40iterations 0.9498084 19.72934 at 50iterations 0.5380949 11.14728 at 60iterations 0.3046698 6.176448 at 70iterations 0.1723403 3.847866 at 80iterations 9.7477026E-02 1.894470 at 90iterations 5.4973956E-02 1.128347 at 100iterations 3.1058237E-02 0.5897913 at 110iterations 1.7595181E-02 0.3442345 at 120iterations 9.9308100E-03 0.1846585 at 130iterations 5.6267371E-03 0.1067924 at 140iterations 3.1825840E-03 6.1485767E-02 at 150iterations 1.8008450E-03 3.4549713E-02 at 160iterations 1.0247813E-03 2.0026565E-02 at 170iterations 5.8501353E-04 1.1379242E-02 at 180iterations finished qdiffx linear iterations at : 07:58:38 total time elapsed so far: 15.11000 # loops : 180 mean,max change (kT/e) : 5.8501353E-04 1.1379242E-02 energy calculations done at 15.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 07:58:39 15.348u 0.245s 0:16.25 95.8% 0+0k 0+0io 0pf+0w