Wed Feb 15 08:53:57 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 08:53:58 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 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: 0.6423327 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): 5.781000 61.20400 ymin,ymax (A): 2.910000 50.09100 zmin,zma (A): 14.63300 55.85800 x,y,z range (A): 55.42300 47.18100 41.22500 scale (grids/A): 0.6423327 object centre (A): 33.49250 26.50050 35.24550 number of atom coordinates read : 2015 total number of charged atoms : 1880 net assigned charge : 1.000007 assigned positive charge : 300.0428 centred at (gu) : 87.12002 89.37539 89.28967 assigned negative charge : -299.0429 centred at (gu) : 87.25896 89.39450 89.33159 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5484 nv = 96 ne = 84 npr = 41634 no. pairs analyzed = 41634 no. exposed pairs = 2610 no. arc points = 18317 no. surface atoms = 882 nbur = 1133 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 2890 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1753 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8698233E-09 -2.4866000E-09 midg,1,midg; midg,igrid,midg 3.2995564E-09 -6.3240352E-10 1,midg,midg; igrid,midg,midg 2.6504493E-08 -6.6139911E-09 gauss-seidel spectral radius is 0.9873893 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 08:53:58 rms-change max change #iterations 0.1224107 20.55515 at 10iterations 1.2479864E-02 2.475325 at 20iterations 1.2451318E-03 0.2160692 at 30iterations 1.3005185E-04 2.1429062E-02 at 40iterations 1.5104191E-05 2.5444031E-03 at 50iterations finished qdiffx linear iterations at : 08:54:01 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 1.5104191E-05 2.5444031E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 08:54:02 3.676u 0.232s 0:04.39 88.8% 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 Wed Feb 15 2012 at 08:54:02 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 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: 1.926998 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): 5.781000 61.20400 ymin,ymax (A): 2.910000 50.09100 zmin,zma (A): 14.63300 55.85800 x,y,z range (A): 55.42300 47.18100 41.22500 scale (grids/A): 1.926998 object centre (A): 33.49250 26.50050 35.24550 number of atom coordinates read : 2015 total number of charged atoms : 1880 net assigned charge : 1.000007 assigned positive charge : 300.0428 centred at (gu) : 81.35985 88.12606 87.86903 assigned negative charge : -299.0429 centred at (gu) : 81.77690 88.18356 87.99445 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18317 grid for indexing accessible points = 1.400000 m= 20667 mr = 39840 m= 3202 mr = 14727 m= 196 mr = 1933 m= 4 mr = 56 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 0.3000000 number of dielectric boundary points 26724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14827 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) : 0.6423327 object centre at (A) : 33.49250 26.50050 35.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5010375E-02 4.4406310E-04 midg,1,midg; midg,igrid,midg 1.4024421E-02 -6.1277620E-04 1,midg,midg; igrid,midg,midg -3.0215424E-02 -4.2051408E-02 gauss-seidel spectral radius is 0.9986022 estimated iterations to convergence 212 setup time was (sec) 0.5100000 now iterating at: 08:54:03 rms-change max change #iterations 3.722646 171.8584 at 10iterations 1.714493 65.47392 at 20iterations 0.7995647 30.46212 at 30iterations 0.3711047 14.76074 at 40iterations 0.1723297 6.999697 at 50iterations 7.9890177E-02 2.666328 at 60iterations 3.6987878E-02 1.278225 at 70iterations 1.7158663E-02 0.5879288 at 80iterations 7.9714684E-03 0.2835693 at 90iterations 3.7005949E-03 0.1483707 at 100iterations 1.7169778E-03 6.4327240E-02 at 110iterations 7.9773413E-04 3.1265616E-02 at 120iterations finished qdiffx linear iterations at : 08:54:10 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 7.9773413E-04 3.1265616E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 08:54:11 7.735u 0.201s 0:08.57 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 Wed Feb 15 2012 at 08:54:11 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: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 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: 2.890497 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): 5.781000 61.20400 ymin,ymax (A): 2.910000 50.09100 zmin,zma (A): 14.63300 55.85800 x,y,z range (A): 55.42300 47.18100 41.22500 scale (grids/A): 2.890497 object centre (A): 33.49250 26.50050 35.24550 number of atom coordinates read : 2015 total number of charged atoms : 1880 net assigned charge : 1.000007 assigned positive charge : 300.0428 centred at (gu) : 77.03972 87.18903 86.80355 assigned negative charge : -299.0429 centred at (gu) : 77.66534 87.27528 86.99178 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 136958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18317 grid for indexing accessible points = 1.400000 m= 67052 mr = 97077 m= 23574 mr = 53680 m= 5710 mr = 18456 m= 822 mr = 4133 m= 53 mr = 530 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 60271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15040 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) : 1.926998 object centre at (A) : 33.49250 26.50050 35.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1685032 -3.8174754E-03 midg,1,midg; midg,igrid,midg 0.1442036 -6.0580082E-02 1,midg,midg; igrid,midg,midg -0.5731779 -0.7342057 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.030000 now iterating at: 08:54:12 rms-change max change #iterations 8.870584 339.2064 at 10iterations 5.157803 120.7080 at 20iterations 2.983042 70.64093 at 30iterations 1.727667 39.12741 at 40iterations 0.9934101 23.04995 at 50iterations 0.5712101 11.42998 at 60iterations 0.3272151 6.566965 at 70iterations 0.1875947 3.793035 at 80iterations 0.1073702 2.476967 at 90iterations 6.1469965E-02 1.199153 at 100iterations 3.5187185E-02 0.7411618 at 110iterations 2.0040434E-02 0.4261918 at 120iterations 1.1460943E-02 0.2477646 at 130iterations 6.5539624E-03 0.1262407 at 140iterations 3.7453054E-03 7.4539185E-02 at 150iterations 2.1420070E-03 4.3117523E-02 at 160iterations 1.2265564E-03 2.4329424E-02 at 170iterations 7.0344954E-04 1.8990517E-02 at 180iterations finished qdiffx linear iterations at : 08:54:23 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 7.0344954E-04 1.8990517E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 08:54:24 12.417u 0.216s 0:13.02 96.9% 0+0k 0+0io 0pf+0w