Thu Jan 19 13:33:09 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:09 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 = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 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: 0.4645215 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 0.4645215 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608944 assigned positive charge : 1013.849 centred at (gu) : 90.13876 88.74966 89.67780 assigned negative charge : -1018.467 centred at (gu) : 90.21873 88.73691 89.63994 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8983 nv = 96 ne = 84 npr = 133607 no. pairs analyzed = 133607 no. exposed pairs = 8815 no. arc points = 59653 no. surface atoms = 2933 nbur = 3767 mkacc time = 0.2400000 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 = 1.820000 m= 275 mr = 4422 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5404 ## 973 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 12197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5014383E-11 8.4484373E-12 midg,1,midg; midg,igrid,midg -1.7287546E-11 -9.4626076E-13 1,midg,midg; igrid,midg,midg 2.5777401E-11 -4.2634514E-11 gauss-seidel spectral radius is 0.9764629 estimated iterations to convergence 54 setup time was (sec) 0.6400000 now iterating at: 13:33:10 rms-change max change #iterations 4.7230985E-02 6.777370 at 10iterations 3.3607800E-03 0.5130205 at 20iterations 1.3151835E-03 0.2191544 at 30iterations 6.1293354E-04 0.1043205 at 40iterations 2.8533276E-04 4.8942566E-02 at 50iterations finished qdiffx linear iterations at : 13:33:16 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 2.8533276E-04 4.8942566E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 13:33:16 3.755u 0.195s 0:07.31 53.8% 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 Thu Jan 19 2012 at 13:33:16 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 = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 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: 1.393565 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 1.393565 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608944 assigned positive charge : 1013.849 centred at (gu) : 90.41451 86.24715 89.03122 assigned negative charge : -1018.467 centred at (gu) : 90.65577 86.21035 88.91956 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 103871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59653 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 27082 mr = 70165 m= 1712 mr = 16706 m= 25 mr = 550 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 766 time to turn everything in is 0.5300000 number of dielectric boundary points 45269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 897 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 47172 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) : 0.4645215 object centre at (A) : 34.71600 -49.56650 8.617502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7008346E-03 1.2509893E-02 midg,1,midg; midg,igrid,midg -7.4128545E-04 -5.2733446E-04 1,midg,midg; igrid,midg,midg 2.8496420E-03 -1.9668737E-02 gauss-seidel spectral radius is 0.9978481 estimated iterations to convergence 172 setup time was (sec) 0.7600000 now iterating at: 13:33:18 rms-change max change #iterations 3.744835 127.0957 at 10iterations 1.446403 45.35338 at 20iterations 0.5578584 17.08983 at 30iterations 0.2159197 6.665298 at 40iterations 8.3401754E-02 3.021711 at 50iterations 3.2421328E-02 1.074425 at 60iterations 1.2789079E-02 0.4250145 at 70iterations 5.2142339E-03 0.1518402 at 80iterations 2.3863257E-03 9.2046738E-02 at 90iterations 1.3228410E-03 5.0765991E-02 at 100iterations 8.7768910E-04 3.1639099E-02 at 110iterations 6.3604681E-04 2.1282196E-02 at 120iterations finished qdiffx linear iterations at : 13:33:33 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 6.3604681E-04 2.1282196E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 13:33:33 8.258u 0.242s 0:16.91 50.2% 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 Thu Jan 19 2012 at 13:33:33 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 = 6700 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 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: 2.090347 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): -3.603000 73.03500 ymin,ymax (A): -83.10900 -16.02400 zmin,zma (A): -28.12000 45.35500 x,y,z range (A): 76.63800 67.08500 73.47501 scale (grids/A): 2.090347 object centre (A): 34.71600 -49.56650 8.617502 number of atom coordinates read : 6700 total number of charged atoms : 6530 net assigned charge : -4.608944 assigned positive charge : 1013.849 centred at (gu) : 90.62107 84.37024 88.54662 assigned negative charge : -1018.467 centred at (gu) : 90.98352 84.31546 88.37935 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 243196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59653 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 101381 mr = 174174 m= 21414 mr = 76541 m= 2058 mr = 14118 m= 68 mr = 954 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2666 time to turn everything in is 1.230000 number of dielectric boundary points 102320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 51860 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) : 1.393565 object centre at (A) : 34.71600 -49.56650 8.617502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2949814 0.4052415 midg,1,midg; midg,igrid,midg -1.6023530E-02 -1.0770567E-02 1,midg,midg; igrid,midg,midg 0.1561129 -0.3282096 gauss-seidel spectral radius is 0.9991222 estimated iterations to convergence 267 setup time was (sec) 1.490000 now iterating at: 13:33:37 rms-change max change #iterations 10.76033 285.7996 at 10iterations 6.069806 144.7331 at 20iterations 3.409690 73.13646 at 30iterations 1.906762 40.45649 at 40iterations 1.060810 23.10722 at 50iterations 0.5871876 12.07172 at 60iterations 0.3248031 6.141531 at 70iterations 0.1797219 3.383888 at 80iterations 9.8935857E-02 2.078163 at 90iterations 5.4402947E-02 1.051086 at 100iterations 2.9904231E-02 0.6073456 at 110iterations 1.6464647E-02 0.3106308 at 120iterations 9.0533104E-03 0.1713963 at 130iterations 5.0003249E-03 8.6970329E-02 at 140iterations 2.7766856E-03 4.9880028E-02 at 150iterations 1.5649041E-03 3.0393600E-02 at 160iterations 9.0987544E-04 1.7730713E-02 at 170iterations 5.5609288E-04 1.1148453E-02 at 180iterations finished qdiffx linear iterations at : 13:34:00 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 5.5609288E-04 1.1148453E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 13:34:00 13.954u 0.291s 0:27.05 52.6% 0+0k 0+0io 0pf+0w