Wed Feb 15 08:57:07 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_thinner.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 Wed Feb 15 2012 at 08:57:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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: 0.6092030 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 0.6092030 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.00533 91.02808 90.59098 assigned negative charge : -386.3415 centred at (gu) : 90.10601 90.99424 90.49160 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5882 nv = 96 ne = 84 npr = 52994 no. pairs analyzed = 52994 no. exposed pairs = 2946 no. arc points = 20938 no. surface atoms = 1004 nbur = 1494 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3181 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2120 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2875296E-09 2.7415710E-09 midg,1,midg; midg,igrid,midg -3.1721605E-09 -8.8175423E-10 1,midg,midg; igrid,midg,midg 2.4370115E-09 -7.2488762E-09 gauss-seidel spectral radius is 0.9860356 estimated iterations to convergence 69 setup time was (sec) 0.8500000 now iterating at: 08:57:08 rms-change max change #iterations 0.1131637 18.92501 at 10iterations 1.0102850E-02 1.515375 at 20iterations 8.8485051E-04 0.1363814 at 30iterations 7.9391371E-05 1.1789322E-02 at 40iterations 7.0238684E-06 1.1662245E-03 at 50iterations finished qdiffx linear iterations at : 08:57:16 total time elapsed so far: 8.510000 # loops : 50 mean,max change (kT/e) : 7.0238684E-06 1.1662245E-03 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 08:57:17 8.668u 0.708s 0:09.84 95.1% 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 Wed Feb 15 2012 at 08:57:17 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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: 1.827609 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 1.827609 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.01556 93.08376 91.77246 assigned negative charge : -386.3415 centred at (gu) : 90.31783 92.98269 91.47452 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20938 grid for indexing accessible points = 1.400000 m= 21739 mr = 44325 m= 3281 mr = 15770 m= 197 mr = 2094 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 27353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18434 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) : 0.6092030 object centre at (A) : 39.53950 25.79500 10.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1056529E-02 8.6570149E-03 midg,1,midg; midg,igrid,midg -6.8977256E-03 1.4885805E-02 1,midg,midg; igrid,midg,midg -1.8363269E-02 -4.5817304E-02 gauss-seidel spectral radius is 0.9985009 estimated iterations to convergence 205 setup time was (sec) 1.170000 now iterating at: 08:57:19 rms-change max change #iterations 3.916031 174.3022 at 10iterations 1.763408 77.54594 at 20iterations 0.7956203 26.89875 at 30iterations 0.3598124 12.36546 at 40iterations 0.1624961 5.441204 at 50iterations 7.3522210E-02 2.599749 at 60iterations 3.3139806E-02 1.125456 at 70iterations 1.4976777E-02 0.5027313 at 80iterations 6.7654918E-03 0.2258606 at 90iterations 3.0621705E-03 0.1055355 at 100iterations 1.3789894E-03 4.6030045E-02 at 110iterations 6.2508835E-04 2.1141052E-02 at 120iterations finished qdiffx linear iterations at : 08:57:37 total time elapsed so far: 19.06000 # loops : 120 mean,max change (kT/e) : 6.2508835E-04 2.1141052E-02 energy calculations done at 19.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.23000 DelPhi exited at 08:57:37 19.240u 0.912s 0:20.52 98.1% 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 Wed Feb 15 2012 at 08:57:37 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.741414 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 2.741414 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.02313 94.62563 92.65857 assigned negative charge : -386.3415 centred at (gu) : 90.47671 94.47393 92.21170 start vw surface at 0.1200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 149370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20938 grid for indexing accessible points = 1.400000 m= 71956 mr = 107954 m= 24380 mr = 58362 m= 5965 mr = 19501 m= 895 mr = 4532 m= 47 mr = 627 m= 0 mr = 10 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 61627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 18863 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) : 1.827609 object centre at (A) : 39.53950 25.79500 10.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1016722 0.1582409 midg,1,midg; midg,igrid,midg -9.7078308E-02 0.2031050 1,midg,midg; igrid,midg,midg -0.5615174 -0.5876465 gauss-seidel spectral radius is 0.9992149 estimated iterations to convergence 282 setup time was (sec) 2.340000 now iterating at: 08:57:41 rms-change max change #iterations 9.214887 305.9378 at 10iterations 5.267268 116.7606 at 20iterations 2.981356 61.75039 at 30iterations 1.691145 34.03558 at 40iterations 0.9558848 22.92001 at 50iterations 0.5399404 12.01270 at 60iterations 0.3045664 6.164362 at 70iterations 0.1717807 3.416018 at 80iterations 9.7025394E-02 1.740315 at 90iterations 5.4689575E-02 1.084879 at 100iterations 3.0917438E-02 0.6772842 at 110iterations 1.7431123E-02 0.3971996 at 120iterations 9.8231025E-03 0.2020249 at 130iterations 5.5512260E-03 0.1075733 at 140iterations 3.1361391E-03 7.2494507E-02 at 150iterations 1.7671394E-03 3.2499075E-02 at 160iterations 9.9585648E-04 2.0500183E-02 at 170iterations 5.6540029E-04 1.1143684E-02 at 180iterations finished qdiffx linear iterations at : 08:58:08 total time elapsed so far: 29.62000 # loops : 180 mean,max change (kT/e) : 5.6540029E-04 1.1143684E-02 energy calculations done at 29.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.79000 DelPhi exited at 08:58:08 29.799u 0.757s 0:30.84 99.0% 0+0k 0+0io 0pf+0w