Tue Oct 11 08:33:23 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 Tue Oct 11 2011 at 08:33:23 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7063492 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 0.7063492 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1913 net assigned charge : 5.945010 assigned positive charge : 311.6111 centred at (gu) : 90.91983 89.84228 91.01509 assigned negative charge : -305.6661 centred at (gu) : 90.85170 89.77551 90.90683 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7016 nv = 96 ne = 84 npr = 40681 no. pairs analyzed = 40681 no. exposed pairs = 2539 no. arc points = 17417 no. surface atoms = 852 nbur = 1195 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4003 m= 0 mr = 96 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1635 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7729 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5267681E-09 1.2018175E-07 midg,1,midg; midg,igrid,midg 1.6678859E-08 7.6942406E-08 1,midg,midg; igrid,midg,midg 1.3439363E-08 9.5553418E-08 gauss-seidel spectral radius is 0.9895511 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 08:33:24 rms-change max change #iterations 0.1974437 24.70648 at 10iterations 2.4480298E-02 3.731525 at 20iterations 3.2829149E-03 0.4188385 at 30iterations 5.7857600E-04 7.4401855E-02 at 40iterations 1.5236503E-04 1.7711639E-02 at 50iterations finished qdiffx linear iterations at : 08:33:26 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.5236503E-04 1.7711639E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:33:27 3.467u 0.154s 0:04.09 88.2% 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 Tue Oct 11 2011 at 08:33:27 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.119048 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 2.119048 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1913 net assigned charge : 5.945010 assigned positive charge : 311.6111 centred at (gu) : 92.75945 89.52679 93.04543 assigned negative charge : -305.6661 centred at (gu) : 92.55505 89.32659 92.72057 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17417 grid for indexing accessible points = 1.400000 m= 30160 mr = 52349 m= 5746 mr = 23015 m= 507 mr = 3806 m= 16 mr = 277 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 31112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15201 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) : 0.7063492 object centre at (A) : 4.641000 9.427500 14.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3542734E-02 3.3700991E-02 midg,1,midg; midg,igrid,midg 1.9844396E-02 1.9240679E-02 1,midg,midg; igrid,midg,midg 5.3420637E-02 3.1579025E-02 gauss-seidel spectral radius is 0.9988275 estimated iterations to convergence 231 setup time was (sec) 0.8700000 now iterating at: 08:33:28 rms-change max change #iterations 4.590767 180.6983 at 10iterations 2.267400 71.84267 at 20iterations 1.125040 36.17268 at 30iterations 0.5571222 16.26705 at 40iterations 0.2757272 8.441528 at 50iterations 0.1370032 4.220220 at 60iterations 6.8351462E-02 2.067352 at 70iterations 3.3888284E-02 1.039186 at 80iterations 1.6850831E-02 0.5051575 at 90iterations 8.5165361E-03 0.2595177 at 100iterations 4.2892038E-03 0.1289263 at 110iterations 2.2187328E-03 7.7298164E-02 at 120iterations finished qdiffx linear iterations at : 08:33:35 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.2187328E-03 7.7298164E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 08:33:36 7.994u 0.187s 0:08.48 96.3% 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 08:33:36 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.178571 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 3.178571 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1913 net assigned charge : 5.945010 assigned positive charge : 311.6111 centred at (gu) : 94.13920 89.29010 94.56815 assigned negative charge : -305.6661 centred at (gu) : 93.83282 88.98989 94.08089 start vw surface at 0.1300000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 170677 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17417 grid for indexing accessible points = 1.400000 m= 93578 mr = 125858 m= 38383 mr = 77969 m= 10714 mr = 31653 m= 2100 mr = 8318 m= 236 mr = 1544 m= 15 mr = 172 m= 0 mr = 4 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 70185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 15304 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) : 2.119048 object centre at (A) : 4.641000 9.427500 14.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3868733 0.2856528 midg,1,midg; midg,igrid,midg 0.1476837 0.1034413 1,midg,midg; igrid,midg,midg 0.4201106 0.1258458 gauss-seidel spectral radius is 0.9992948 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 08:33:38 rms-change max change #iterations 10.17441 405.3599 at 10iterations 5.988180 121.4707 at 20iterations 3.532214 69.66846 at 30iterations 2.076627 40.57328 at 40iterations 1.218436 23.54345 at 50iterations 0.7158669 13.87185 at 60iterations 0.4192199 9.641464 at 70iterations 0.2461984 4.173258 at 80iterations 0.1439031 2.488819 at 90iterations 8.4474362E-02 1.601322 at 100iterations 4.9768742E-02 0.9314685 at 110iterations 2.9402303E-02 0.5851669 at 120iterations 1.7573761E-02 0.4094696 at 130iterations 1.0721917E-02 0.2064018 at 140iterations 6.7770337E-03 0.1535416 at 150iterations 4.4781198E-03 9.0621948E-02 at 160iterations 3.1453881E-03 6.1912537E-02 at 170iterations 2.3401703E-03 4.7676086E-02 at 180iterations finished qdiffx linear iterations at : 08:33:49 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 2.3401703E-03 4.7676086E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 08:33:50 12.777u 0.246s 0:13.93 93.3% 0+0k 0+0io 0pf+0w