Tue Oct 11 05:16:42 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 Tue Oct 11 2011 at 05:16:42 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6900562 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 0.6900562 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 326.5739 centred at (gu) : 91.41344 89.64912 89.16415 assigned negative charge : -317.5741 centred at (gu) : 91.51528 89.65672 89.08929 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6807 nv = 96 ne = 84 npr = 42732 no. pairs analyzed = 42732 no. exposed pairs = 2598 no. arc points = 17701 no. surface atoms = 882 nbur = 1438 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3916 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1712 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9181761E-08 6.4178074E-08 midg,1,midg; midg,igrid,midg 5.6797990E-08 4.4835588E-08 1,midg,midg; igrid,midg,midg 6.4100533E-08 2.0026601E-08 gauss-seidel spectral radius is 0.9890611 estimated iterations to convergence 78 setup time was (sec) 0.6500000 now iterating at: 05:16:42 rms-change max change #iterations 0.1877643 27.60269 at 10iterations 2.1743359E-02 2.841858 at 20iterations 2.5684040E-03 0.3572174 at 30iterations 3.0387679E-04 4.0374756E-02 at 40iterations 3.6391550E-05 4.9648285E-03 at 50iterations finished qdiffx linear iterations at : 05:16:46 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.6391550E-05 4.9648285E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 05:16:47 4.194u 0.219s 0:05.00 88.0% 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 05:16:47 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.070169 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 2.070169 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 326.5739 centred at (gu) : 94.24020 88.94724 87.49258 assigned negative charge : -317.5741 centred at (gu) : 94.54602 88.97029 87.26792 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 72142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17701 grid for indexing accessible points = 1.400000 m= 28797 mr = 50987 m= 5640 mr = 21921 m= 486 mr = 3762 m= 10 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.7000000 number of dielectric boundary points 30166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15840 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) : 0.6900562 object centre at (A) : 39.34500 15.08300 45.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7846545E-02 4.7726385E-02 midg,1,midg; midg,igrid,midg 2.8416442E-02 2.4019135E-02 1,midg,midg; igrid,midg,midg 2.7092321E-02 3.1584702E-02 gauss-seidel spectral radius is 0.9987816 estimated iterations to convergence 227 setup time was (sec) 1.040000 now iterating at: 05:16:48 rms-change max change #iterations 4.466365 238.2841 at 10iterations 2.192263 72.99979 at 20iterations 1.060837 39.72360 at 30iterations 0.5223415 15.47716 at 40iterations 0.2544134 7.956749 at 50iterations 0.1244988 3.651734 at 60iterations 6.0878612E-02 2.092594 at 70iterations 2.9693631E-02 0.8584454 at 80iterations 1.4543731E-02 0.4939604 at 90iterations 7.0994212E-03 0.2428665 at 100iterations 3.4707356E-03 0.1151733 at 110iterations 1.6976978E-03 5.4771423E-02 at 120iterations finished qdiffx linear iterations at : 05:16:56 total time elapsed so far: 8.660000 # loops : 120 mean,max change (kT/e) : 1.6976978E-03 5.4771423E-02 energy calculations done at 8.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 05:16:56 8.895u 0.187s 0:09.39 96.5% 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 05:16:56 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.105253 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 3.105253 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 326.5739 centred at (gu) : 96.36024 88.42081 86.23878 assigned negative charge : -317.5741 centred at (gu) : 96.81901 88.45544 85.90193 start vw surface at 0.1900000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 166140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17701 grid for indexing accessible points = 1.400000 m= 90058 mr = 122585 m= 36179 mr = 75036 m= 10478 mr = 29755 m= 2042 mr = 8192 m= 206 mr = 1515 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 2.220000 number of dielectric boundary points 67908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 15968 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) : 2.070169 object centre at (A) : 39.34500 15.08300 45.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4394711 0.3616361 midg,1,midg; midg,igrid,midg 0.2520103 0.2156605 1,midg,midg; igrid,midg,midg 0.2230047 0.5448070 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 2.620000 now iterating at: 05:16:59 rms-change max change #iterations 10.12253 378.1315 at 10iterations 5.957160 141.8068 at 20iterations 3.507896 81.88226 at 30iterations 2.060581 45.99163 at 40iterations 1.205562 26.37133 at 50iterations 0.7065343 14.96585 at 60iterations 0.4120989 7.529825 at 70iterations 0.2406061 5.124859 at 80iterations 0.1405924 2.578844 at 90iterations 8.2056344E-02 1.635151 at 100iterations 4.7851842E-02 0.8315887 at 110iterations 2.7864154E-02 0.4982421 at 120iterations 1.6207874E-02 0.2932014 at 130iterations 9.4811162E-03 0.1697845 at 140iterations 5.5317073E-03 9.8316193E-02 at 150iterations 3.2367490E-03 5.8670044E-02 at 160iterations 1.9014569E-03 3.7715912E-02 at 170iterations 1.1320459E-03 2.1150589E-02 at 180iterations finished qdiffx linear iterations at : 05:17:13 total time elapsed so far: 16.20000 # loops : 180 mean,max change (kT/e) : 1.1320459E-03 2.1150589E-02 energy calculations done at 16.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.43000 DelPhi exited at 05:17:13 16.436u 0.228s 0:17.25 96.5% 0+0k 0+0io 0pf+0w