Sun Oct 9 14:54:19 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 Sun Oct 9 2011 at 14:54:19 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7284185 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 0.7284185 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 179.0483 centred at (gu) : 89.60154 89.84359 92.20548 assigned negative charge : -177.5481 centred at (gu) : 89.59994 89.65554 92.11033 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4756 nv = 96 ne = 84 npr = 24425 no. pairs analyzed = 24425 no. exposed pairs = 1702 no. arc points = 12676 no. surface atoms = 570 nbur = 675 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 279 mr = 2419 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.1300000 number of dielectric boundary points 2566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1000 ## 95 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4725 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4553573E-08 9.3772080E-08 midg,1,midg; midg,igrid,midg -6.6961391E-08 9.8114107E-08 1,midg,midg; igrid,midg,midg 2.0332436E-08 1.8899508E-08 gauss-seidel spectral radius is 0.9901009 estimated iterations to convergence 82 setup time was (sec) 0.3100000 now iterating at: 14:54:20 rms-change max change #iterations 0.1766001 35.45292 at 10iterations 2.2955453E-02 3.716197 at 20iterations 2.8541950E-03 0.4543991 at 30iterations 3.6748237E-04 6.9031715E-02 at 40iterations 4.7180678E-05 7.4491501E-03 at 50iterations finished qdiffx linear iterations at : 14:54:23 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.7180678E-05 7.4491501E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:54:23 3.315u 0.182s 0:03.76 92.8% 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 Sun Oct 9 2011 at 14:54:23 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.185256 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 2.185256 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 179.0483 centred at (gu) : 88.80496 89.53104 96.61669 assigned negative charge : -177.5481 centred at (gu) : 88.79988 88.96687 96.33104 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12676 grid for indexing accessible points = 1.400000 m= 18648 mr = 31539 m= 3760 mr = 13872 m= 286 mr = 2590 m= 2 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3216 time to turn everything in is 0.2600000 number of dielectric boundary points 23787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8877 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) : 0.7284185 object centre at (A) : 67.43350 -6.513000 -7.643999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0903557E-03 1.2368278E-02 midg,1,midg; midg,igrid,midg -1.6112452E-03 2.9484674E-02 1,midg,midg; igrid,midg,midg 1.5750349E-02 1.6807139E-02 gauss-seidel spectral radius is 0.9988196 estimated iterations to convergence 230 setup time was (sec) 0.4700000 now iterating at: 14:54:24 rms-change max change #iterations 3.619407 175.3248 at 10iterations 1.776860 70.13751 at 20iterations 0.8717347 34.72615 at 30iterations 0.4295560 16.93570 at 40iterations 0.2108332 7.806818 at 50iterations 0.1041687 3.991850 at 60iterations 5.1226415E-02 1.866678 at 70iterations 2.5118209E-02 1.073402 at 80iterations 1.2400310E-02 0.4691913 at 90iterations 6.1253882E-03 0.2441406 at 100iterations 3.0121040E-03 0.1138840 at 110iterations 1.4885766E-03 5.3203583E-02 at 120iterations finished qdiffx linear iterations at : 14:54:31 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.4885766E-03 5.3203583E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 14:54:31 7.616u 0.200s 0:08.08 96.6% 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 Sun Oct 9 2011 at 14:54:31 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1245 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.277883 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): 42.99700 91.87000 ymin,ymax (A): -27.94300 14.91700 zmin,zma (A): -31.71700 16.42900 x,y,z range (A): 48.87300 42.86000 48.14600 scale (grids/A): 3.277883 object centre (A): 67.43350 -6.513000 -7.643999 number of atom coordinates read : 1245 total number of charged atoms : 1115 net assigned charge : 1.500005 assigned positive charge : 179.0483 centred at (gu) : 88.20745 89.29657 99.92500 assigned negative charge : -177.5481 centred at (gu) : 88.19984 88.45026 99.49660 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 113096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12676 grid for indexing accessible points = 1.400000 m= 57541 mr = 76448 m= 23788 mr = 46835 m= 7183 mr = 19470 m= 1201 mr = 5670 m= 98 mr = 813 m= 4 mr = 72 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 10612 time to turn everything in is 0.7700000 number of dielectric boundary points 53601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 8916 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) : 2.185256 object centre at (A) : 67.43350 -6.513000 -7.643999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5406773E-02 0.4010346 midg,1,midg; midg,igrid,midg -2.9630717E-02 0.2103088 1,midg,midg; igrid,midg,midg 0.1941730 0.1828756 gauss-seidel spectral radius is 0.9993028 estimated iterations to convergence 299 setup time was (sec) 1.010000 now iterating at: 14:54:33 rms-change max change #iterations 8.093594 709.6413 at 10iterations 4.786919 118.0450 at 20iterations 2.826553 69.72486 at 30iterations 1.658506 39.60117 at 40iterations 0.9709098 22.63166 at 50iterations 0.5698700 13.37206 at 60iterations 0.3338259 7.606384 at 70iterations 0.1949655 4.941936 at 80iterations 0.1141386 2.752929 at 90iterations 6.6455841E-02 1.445072 at 100iterations 3.8849358E-02 0.7572179 at 110iterations 2.2613622E-02 0.4659271 at 120iterations 1.3238695E-02 0.2769125 at 130iterations 7.7093462E-03 0.1711264 at 140iterations 4.4868155E-03 9.2300415E-02 at 150iterations 2.6193990E-03 5.5561781E-02 at 160iterations 1.5287120E-03 3.0447006E-02 at 170iterations 8.9273922E-04 1.8190384E-02 at 180iterations finished qdiffx linear iterations at : 14:54:45 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 8.9273922E-04 1.8190384E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 14:54:45 13.327u 0.197s 0:13.79 97.9% 0+0k 0+0io 0pf+0w