Wed Nov 9 23:19:02 PST 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+sph.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 Nov 9 2011 at 23:19:02 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: 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 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5558 nv = 96 ne = 84 npr = 40851 no. pairs analyzed = 40851 no. exposed pairs = 2592 no. arc points = 18276 no. surface atoms = 871 nbur = 1144 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 2969 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2700000 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 0.9873906 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 23:19:02 rms-change max change #iterations 0.1227951 20.74348 at 10iterations 1.2740538E-02 2.416012 at 20iterations 1.2681324E-03 0.2150183 at 30iterations 1.3009569E-04 2.0233154E-02 at 40iterations 1.5731712E-05 2.7494431E-03 at 50iterations finished qdiffx linear iterations at : 23:19:05 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.5731712E-05 2.7494431E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 23:19:06 3.482u 0.186s 0:04.78 76.5% 0+0k 0+45592io 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 Nov 9 2011 at 23:19:07 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: 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= 5.0000001E-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 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18276 grid for indexing accessible points = 1.400000 m= 20965 mr = 40739 m= 3261 mr = 14965 m= 209 mr = 1951 m= 4 mr = 57 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 0.3800000 number of dielectric boundary points 26783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4600000 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 1.5490388E-02 5.1958783E-04 midg,1,midg; midg,igrid,midg 1.4169557E-02 -8.7520754E-04 1,midg,midg; igrid,midg,midg -2.9911796E-02 -4.2079665E-02 gauss-seidel spectral radius is 0.9986033 estimated iterations to convergence 212 setup time was (sec) 0.5900000 now iterating at: 23:19:07 rms-change max change #iterations 3.726554 171.9130 at 10iterations 1.719061 59.70182 at 20iterations 0.8016208 29.80140 at 30iterations 0.3719230 13.12450 at 40iterations 0.1729452 6.018166 at 50iterations 8.0120377E-02 2.894731 at 60iterations 3.7111841E-02 1.341370 at 70iterations 1.7283699E-02 0.5970809 at 80iterations 8.0248406E-03 0.3030949 at 90iterations 3.7245692E-03 0.1264057 at 100iterations 1.7279221E-03 5.8950901E-02 at 110iterations 8.0554682E-04 3.0623436E-02 at 120iterations finished qdiffx linear iterations at : 23:19:15 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 8.0554682E-04 3.0623436E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 23:19:15 7.923u 0.202s 0:08.58 94.6% 0+0k 0+45152io 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 Nov 9 2011 at 23:19:15 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= 5.0000001E-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 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 138961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18276 grid for indexing accessible points = 1.400000 m= 68262 mr = 99294 m= 23893 mr = 54780 m= 5815 mr = 18655 m= 872 mr = 4175 m= 56 mr = 550 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 60383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 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 0.1747915 -3.1472254E-03 midg,1,midg; midg,igrid,midg 0.1453913 -6.7667559E-02 1,midg,midg; igrid,midg,midg -0.5706317 -0.7335753 gauss-seidel spectral radius is 0.9992413 estimated iterations to convergence 287 setup time was (sec) 1.220000 now iterating at: 23:19:17 rms-change max change #iterations 8.873443 339.1156 at 10iterations 5.163800 120.6471 at 20iterations 2.987295 70.38586 at 30iterations 1.727308 38.89854 at 40iterations 0.9951105 23.67760 at 50iterations 0.5713598 11.68397 at 60iterations 0.3278788 6.648755 at 70iterations 0.1877410 3.959198 at 80iterations 0.1072909 2.290092 at 90iterations 6.1436865E-02 1.161299 at 100iterations 3.5106290E-02 0.7431164 at 110iterations 2.0026576E-02 0.3912020 at 120iterations 1.1465286E-02 0.2445498 at 130iterations 6.5497048E-03 0.1444778 at 140iterations 3.7467664E-03 7.7767849E-02 at 150iterations 2.1414561E-03 4.3571472E-02 at 160iterations 1.2252566E-03 2.7192116E-02 at 170iterations 7.0502813E-04 1.7048836E-02 at 180iterations finished qdiffx linear iterations at : 23:19:28 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 7.0502813E-04 1.7048836E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 23:19:33 12.581u 0.207s 0:17.96 71.1% 0+0k 0+45144io 0pf+0w