Mon Oct 10 14:00:53 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 14:00:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4641097 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 0.4641097 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.999978 assigned positive charge : 937.7590 centred at (gu) : 89.90749 88.84108 89.27472 assigned negative charge : -941.7675 centred at (gu) : 89.83229 88.86406 89.16467 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8162 nv = 96 ne = 84 npr = 126024 no. pairs analyzed = 126024 no. exposed pairs = 7715 no. arc points = 53169 no. surface atoms = 2595 nbur = 3622 mkacc time = 0.2700000 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 = 1.848000 m= 244 mr = 4128 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4937 ## 953 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 11237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9848002E-11 2.9129692E-11 midg,1,midg; midg,igrid,midg 4.6971389E-12 -1.0320016E-11 1,midg,midg; igrid,midg,midg -3.5628580E-11 2.2384847E-11 gauss-seidel spectral radius is 0.9763817 estimated iterations to convergence 54 setup time was (sec) 0.8200000 now iterating at: 14:00:54 rms-change max change #iterations 4.6423223E-02 7.364773 at 10iterations 2.1268723E-03 0.3232307 at 20iterations 2.0557920E-04 5.7632446E-02 at 30iterations 4.6629364E-05 1.3498306E-02 at 40iterations 1.2569402E-05 3.3779144E-03 at 50iterations finished qdiffx linear iterations at : 14:00:57 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.2569402E-05 3.3779144E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 14:00:59 3.705u 0.195s 0:05.70 68.2% 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 14:00:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.392329 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 1.392329 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.999978 assigned positive charge : 937.7590 centred at (gu) : 89.72019 86.52127 87.82232 assigned negative charge : -941.7675 centred at (gu) : 89.49648 86.59184 87.49385 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 94338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53169 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 23577 mr = 64139 m= 1351 mr = 14492 m= 10 mr = 401 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 961 time to turn everything in is 0.6700000 number of dielectric boundary points 40244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 908 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 43679 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) : 0.4641097 object centre at (A) : 42.02400 53.84400 38.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0300325E-03 4.3004067E-03 midg,1,midg; midg,igrid,midg -1.3954899E-03 -2.4400209E-03 1,midg,midg; igrid,midg,midg -6.7417184E-03 -5.3277686E-03 gauss-seidel spectral radius is 0.9977883 estimated iterations to convergence 169 setup time was (sec) 0.9400000 now iterating at: 14:01:00 rms-change max change #iterations 3.506846 167.5212 at 10iterations 1.331989 41.89038 at 20iterations 0.5103105 17.17245 at 30iterations 0.1948941 6.703822 at 40iterations 7.4491248E-02 2.597281 at 50iterations 2.8449509E-02 0.9587164 at 60iterations 1.0930330E-02 0.3610134 at 70iterations 4.1714148E-03 0.1361275 at 80iterations 1.6014453E-03 5.1836014E-02 at 90iterations 6.1744038E-04 2.1791458E-02 at 100iterations 2.4098739E-04 8.5535049E-03 at 110iterations 9.6462172E-05 3.3473969E-03 at 120iterations finished qdiffx linear iterations at : 14:01:06 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 9.6462172E-05 3.3473969E-03 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 14:01:07 7.290u 0.207s 0:08.35 89.7% 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 14:01:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.088494 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 2.088494 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.999978 assigned positive charge : 937.7590 centred at (gu) : 89.57985 84.78133 86.73303 assigned negative charge : -941.7675 centred at (gu) : 89.24462 84.88799 86.24082 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 221004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53169 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 90274 mr = 159044 m= 17832 mr = 68086 m= 1601 mr = 11814 m= 32 mr = 750 m= 0 mr = 6 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3243 time to turn everything in is 1.510000 number of dielectric boundary points 91043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 48012 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) : 1.392329 object centre at (A) : 42.02400 53.84400 38.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2309996E-02 5.9448633E-02 midg,1,midg; midg,igrid,midg -1.0635605E-02 -3.1764314E-02 1,midg,midg; igrid,midg,midg -2.4768038E-02 -0.5363975 gauss-seidel spectral radius is 0.9990992 estimated iterations to convergence 263 setup time was (sec) 1.810000 now iterating at: 14:01:09 rms-change max change #iterations 10.26567 283.9110 at 10iterations 5.810449 142.3600 at 20iterations 3.267978 73.91075 at 30iterations 1.820684 49.75301 at 40iterations 1.012211 22.66330 at 50iterations 0.5605996 12.07813 at 60iterations 0.3094199 7.604948 at 70iterations 0.1706392 3.884066 at 80iterations 9.3797877E-02 1.869098 at 90iterations 5.1418096E-02 0.9779396 at 100iterations 2.8231347E-02 0.5294571 at 110iterations 1.5458630E-02 0.3149649 at 120iterations 8.4602470E-03 0.1701393 at 130iterations 4.6251016E-03 8.7929726E-02 at 140iterations 2.5307632E-03 4.9211025E-02 at 150iterations 1.3826508E-03 2.8468132E-02 at 160iterations 7.5759948E-04 1.4390856E-02 at 170iterations 4.1553754E-04 8.3999634E-03 at 180iterations finished qdiffx linear iterations at : 14:01:22 total time elapsed so far: 14.22000 # loops : 180 mean,max change (kT/e) : 4.1553754E-04 8.3999634E-03 energy calculations done at 14.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.42000 DelPhi exited at 14:01:23 14.421u 0.213s 0:15.85 92.3% 0+0k 0+0io 0pf+0w