Sat Oct 8 11:38:13 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+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 Sat Oct 8 2011 at 11:38:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 0.5947111 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 0.5947111 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000083 assigned positive charge : 421.7383 centred at (gu) : 90.73898 89.33172 88.44964 assigned negative charge : -421.2392 centred at (gu) : 90.71347 89.33826 88.42115 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6890 nv = 96 ne = 84 npr = 56066 no. pairs analyzed = 56066 no. exposed pairs = 4028 no. arc points = 28876 no. surface atoms = 1330 nbur = 1539 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 328 mr = 3341 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2856 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1124009E-09 7.9715673E-10 midg,1,midg; midg,igrid,midg 4.7276072E-10 -2.5933873E-11 1,midg,midg; igrid,midg,midg -5.6195348E-10 1.2323572E-09 gauss-seidel spectral radius is 0.9854041 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 11:38:14 rms-change max change #iterations 0.1071922 15.87647 at 10iterations 8.8407081E-03 1.307287 at 20iterations 7.3962141E-04 0.1213989 at 30iterations 6.1163359E-05 9.0370178E-03 at 40iterations 5.1754737E-06 9.7084045E-04 at 50iterations finished qdiffx linear iterations at : 11:38:18 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 5.1754737E-06 9.7084045E-04 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 11:38:18 4.509u 0.386s 0:05.21 93.6% 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 Sat Oct 8 2011 at 11:38:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 1.784133 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 1.784133 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000083 assigned positive charge : 421.7383 centred at (gu) : 92.21648 87.99425 85.34789 assigned negative charge : -421.2392 centred at (gu) : 92.14001 88.01421 85.26292 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28876 grid for indexing accessible points = 1.400000 m= 24523 mr = 48465 m= 3247 mr = 16536 m= 163 mr = 1715 m= 0 mr = 45 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 363 time to turn everything in is 0.6100000 number of dielectric boundary points 35664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21185 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) : 0.5947111 object centre at (A) : 2.725499 19.94550 25.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0245222E-02 1.7706684E-03 midg,1,midg; midg,igrid,midg 1.2772105E-02 6.8307118E-03 1,midg,midg; igrid,midg,midg -2.6361495E-03 -1.3974254E-02 gauss-seidel spectral radius is 0.9984950 estimated iterations to convergence 204 setup time was (sec) 0.9600000 now iterating at: 11:38:20 rms-change max change #iterations 3.879752 161.2369 at 10iterations 1.752716 57.00968 at 20iterations 0.7844776 25.88121 at 30iterations 0.3524314 12.13690 at 40iterations 0.1588162 5.611300 at 50iterations 7.1291648E-02 2.480173 at 60iterations 3.2017924E-02 1.095510 at 70iterations 1.4483768E-02 0.5090027 at 80iterations 6.4973808E-03 0.2330837 at 90iterations 2.9346624E-03 0.1050596 at 100iterations 1.3250259E-03 4.3769836E-02 at 110iterations 5.9803971E-04 1.9271851E-02 at 120iterations finished qdiffx linear iterations at : 11:38:29 total time elapsed so far: 10.48000 # loops : 120 mean,max change (kT/e) : 5.9803971E-04 1.9271851E-02 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 11:38:30 10.650u 0.474s 0:11.46 97.0% 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 11:38:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 2.676200 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 2.676200 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000083 assigned positive charge : 421.7383 centred at (gu) : 93.32459 86.99116 83.02183 assigned negative charge : -421.2392 centred at (gu) : 93.20987 87.02118 82.89432 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 172119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28876 grid for indexing accessible points = 1.400000 m= 81220 mr = 118498 m= 25998 mr = 63148 m= 5330 mr = 19272 m= 657 mr = 3672 m= 25 mr = 383 m= 0 mr = 6 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1253 time to turn everything in is 1.560000 number of dielectric boundary points 80370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 21738 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) : 1.784133 object centre at (A) : 2.725499 19.94550 25.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1403575 -4.9608834E-02 midg,1,midg; midg,igrid,midg 0.1776957 6.7003921E-02 1,midg,midg; igrid,midg,midg 0.4230381 -0.1752203 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.900000 now iterating at: 11:38:32 rms-change max change #iterations 9.727601 305.8162 at 10iterations 5.796938 144.9866 at 20iterations 3.393771 76.82110 at 30iterations 1.976864 40.99284 at 40iterations 1.146091 26.93396 at 50iterations 0.6639137 13.65404 at 60iterations 0.3828950 7.555785 at 70iterations 0.2202809 4.572678 at 80iterations 0.1262444 2.384068 at 90iterations 7.2631009E-02 1.369205 at 100iterations 4.1578170E-02 0.8127420 at 110iterations 2.3786535E-02 0.4341636 at 120iterations 1.3593587E-02 0.2679691 at 130iterations 7.7772895E-03 0.1451142 at 140iterations 4.4501093E-03 8.4141731E-02 at 150iterations 2.5414543E-03 4.6763897E-02 at 160iterations 1.4491410E-03 2.6663423E-02 at 170iterations 8.3078584E-04 1.6285896E-02 at 180iterations finished qdiffx linear iterations at : 11:38:49 total time elapsed so far: 18.20000 # loops : 180 mean,max change (kT/e) : 8.3078584E-04 1.6285896E-02 energy calculations done at 18.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.36000 DelPhi exited at 11:38:49 18.367u 0.499s 0:19.30 97.6% 0+0k 0+0io 0pf+0w