Sat Oct 8 19:07:01 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 Sat Oct 8 2011 at 19:07:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6261652 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): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 0.6261652 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2471 net assigned charge : 5.406007 assigned positive charge : 396.5021 centred at (gu) : 88.48502 89.22897 90.04122 assigned negative charge : -391.0965 centred at (gu) : 88.40694 89.28356 89.89939 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 54400 no. pairs analyzed = 54400 no. exposed pairs = 3036 no. arc points = 21728 no. surface atoms = 1019 nbur = 1596 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3835 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 175 time to turn everything in is 0.2000000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1242265E-09 1.6585721E-08 midg,1,midg; midg,igrid,midg 1.1387595E-08 8.2074703E-10 1,midg,midg; igrid,midg,midg -1.5046030E-09 8.2845828E-09 gauss-seidel spectral radius is 0.9867881 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 19:07:02 rms-change max change #iterations 0.1333568 19.05763 at 10iterations 1.2741721E-02 2.410625 at 20iterations 1.2050989E-03 0.1798363 at 30iterations 1.1221524E-04 1.5962601E-02 at 40iterations 1.0858435E-05 1.6808510E-03 at 50iterations finished qdiffx linear iterations at : 19:07:05 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.0858435E-05 1.6808510E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 19:07:05 3.546u 0.181s 0:04.02 92.5% 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 Sat Oct 8 2011 at 19:07:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.878496 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): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 1.878496 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2471 net assigned charge : 5.406007 assigned positive charge : 396.5021 centred at (gu) : 85.45463 87.68647 90.12310 assigned negative charge : -391.0965 centred at (gu) : 85.22074 87.85040 89.69792 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21728 grid for indexing accessible points = 1.400000 m= 26312 mr = 51679 m= 4039 mr = 19749 m= 254 mr = 2607 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7080 time to turn everything in is 0.3600000 number of dielectric boundary points 29938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19421 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) : 0.6261652 object centre at (A) : -7.158000 -0.3459997 15.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6157953E-02 4.2035319E-02 midg,1,midg; midg,igrid,midg 1.0699796E-02 -4.3212855E-04 1,midg,midg; igrid,midg,midg 2.2072715E-03 3.5452273E-02 gauss-seidel spectral radius is 0.9985962 estimated iterations to convergence 212 setup time was (sec) 0.6100000 now iterating at: 19:07:06 rms-change max change #iterations 4.145965 171.3522 at 10iterations 1.920305 68.63629 at 20iterations 0.8879750 27.37055 at 30iterations 0.4114386 12.89525 at 40iterations 0.1912850 6.106597 at 50iterations 8.8707581E-02 2.966112 at 60iterations 4.0985249E-02 1.336061 at 70iterations 1.8985815E-02 0.5832787 at 80iterations 8.8035082E-03 0.2599907 at 90iterations 4.0790057E-03 0.1264167 at 100iterations 1.8940241E-03 5.8660507E-02 at 110iterations 8.7988272E-04 2.9603958E-02 at 120iterations finished qdiffx linear iterations at : 19:07:14 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 8.7988272E-04 2.9603958E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 19:07:14 8.136u 0.205s 0:08.64 96.4% 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 Sat Oct 8 2011 at 19:07:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.817744 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): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 2.817744 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2471 net assigned charge : 5.406007 assigned positive charge : 396.5021 centred at (gu) : 83.18180 86.52953 90.18462 assigned negative charge : -391.0965 centred at (gu) : 82.83117 86.77551 89.54676 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 169747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21728 grid for indexing accessible points = 1.400000 m= 85878 mr = 124424 m= 30412 mr = 71377 m= 7204 mr = 24701 m= 1129 mr = 5554 m= 51 mr = 810 m= 0 mr = 18 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 24475 time to turn everything in is 0.9300000 number of dielectric boundary points 67537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19765 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) : 1.878496 object centre at (A) : -7.158000 -0.3459997 15.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5626965E-02 0.4525681 midg,1,midg; midg,igrid,midg 0.1150636 -1.8684911E-02 1,midg,midg; igrid,midg,midg 3.4266099E-02 0.4398403 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 19:07:16 rms-change max change #iterations 9.707927 294.2559 at 10iterations 5.585304 122.9581 at 20iterations 3.195939 70.23457 at 30iterations 1.832359 39.49488 at 40iterations 1.045400 19.25509 at 50iterations 0.5967279 12.75864 at 60iterations 0.3403454 6.171420 at 70iterations 0.1942274 3.964641 at 80iterations 0.1109170 2.131330 at 90iterations 6.3183680E-02 1.140656 at 100iterations 3.6036387E-02 0.6909122 at 110iterations 2.0482274E-02 0.4006538 at 120iterations 1.1686900E-02 0.2099228 at 130iterations 6.6665388E-03 0.1270108 at 140iterations 3.7988147E-03 7.3319912E-02 at 150iterations 2.1694938E-03 4.0095329E-02 at 160iterations 1.2361803E-03 2.1888733E-02 at 170iterations 7.0459925E-04 1.3279915E-02 at 180iterations finished qdiffx linear iterations at : 19:07:27 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 7.0459925E-04 1.3279915E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 19:07:28 13.179u 0.223s 0:13.67 97.9% 0+0k 0+0io 0pf+0w