Sun Oct 9 21:03:08 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 Sun Oct 9 2011 at 21:03:08 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 = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 0.6312729 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 0.6312729 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 91.46226 89.02042 90.15334 assigned negative charge : -370.8497 centred at (gu) : 91.53021 88.97510 90.09878 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6469 nv = 96 ne = 84 npr = 51023 no. pairs analyzed = 51023 no. exposed pairs = 3098 no. arc points = 21998 no. surface atoms = 1048 nbur = 1451 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3442 m= 6 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.3200000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8006 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5174335E-10 1.0850644E-08 midg,1,midg; midg,igrid,midg 2.1423738E-09 7.8762765E-09 1,midg,midg; igrid,midg,midg 8.5303995E-09 -4.2967718E-10 gauss-seidel spectral radius is 0.9869925 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 21:03:08 rms-change max change #iterations 0.1324953 19.59494 at 10iterations 1.2642077E-02 2.327428 at 20iterations 1.2183218E-03 0.2119217 at 30iterations 1.1615155E-04 1.7230988E-02 at 40iterations 1.1127458E-05 1.5487671E-03 at 50iterations finished qdiffx linear iterations at : 21:03:11 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1127458E-05 1.5487671E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 21:03:12 3.406u 0.139s 0:03.85 91.6% 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 Sun Oct 9 2011 at 21:03:12 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 = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.893819 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 1.893819 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 94.38630 87.06068 90.45971 assigned negative charge : -370.8497 centred at (gu) : 94.59062 86.92517 90.29613 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 23245 mr = 47492 m= 3548 mr = 16589 m= 224 mr = 2177 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1449 time to turn everything in is 0.5300000 number of dielectric boundary points 30917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18525 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) : 0.6312729 object centre at (A) : -11.74100 9.960501 9.478001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9113282E-02 2.3238802E-02 midg,1,midg; midg,igrid,midg -1.6493587E-02 -2.2951034E-03 1,midg,midg; igrid,midg,midg 4.5798719E-02 1.3813087E-03 gauss-seidel spectral radius is 0.9986032 estimated iterations to convergence 212 setup time was (sec) 0.8100000 now iterating at: 21:03:13 rms-change max change #iterations 4.043462 164.4435 at 10iterations 1.862659 67.68866 at 20iterations 0.8630041 29.01939 at 30iterations 0.4011795 13.56994 at 40iterations 0.1858054 6.142732 at 50iterations 8.6308680E-02 3.127586 at 60iterations 3.9890680E-02 1.216672 at 70iterations 1.8525636E-02 0.6216316 at 80iterations 8.6021209E-03 0.3100958 at 90iterations 3.9794622E-03 0.1370678 at 100iterations 1.8522837E-03 5.8856964E-02 at 110iterations 8.5912796E-04 3.0279160E-02 at 120iterations finished qdiffx linear iterations at : 21:03:19 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 8.5912796E-04 3.0279160E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 21:03:20 7.735u 0.159s 0:08.22 95.8% 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 Sun Oct 9 2011 at 21:03:20 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 = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.840728 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 2.840728 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 96.57944 85.59085 90.68938 assigned negative charge : -370.8497 centred at (gu) : 96.88577 85.38768 90.44410 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 76482 mr = 115736 m= 26035 mr = 61419 m= 6314 mr = 20371 m= 1039 mr = 4705 m= 65 mr = 753 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 4956 time to turn everything in is 1.290000 number of dielectric boundary points 69664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18844 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) : 1.893819 object centre at (A) : -11.74100 9.960501 9.478001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2581860 0.1920547 midg,1,midg; midg,igrid,midg -0.1338744 -5.0935619E-02 1,midg,midg; igrid,midg,midg 0.5027065 -5.0573424E-02 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.600000 now iterating at: 21:03:22 rms-change max change #iterations 9.447555 325.1550 at 10iterations 5.454537 118.6543 at 20iterations 3.125221 59.76035 at 30iterations 1.790373 39.38910 at 40iterations 1.023772 19.99118 at 50iterations 0.5844519 11.17131 at 60iterations 0.3346413 6.171345 at 70iterations 0.1912305 3.681659 at 80iterations 0.1091968 2.226614 at 90iterations 6.2370967E-02 1.229400 at 100iterations 3.5665136E-02 0.6989632 at 110iterations 2.0295357E-02 0.3688412 at 120iterations 1.1608761E-02 0.2280040 at 130iterations 6.6239904E-03 0.1293411 at 140iterations 3.7851671E-03 6.6062927E-02 at 150iterations 2.1631806E-03 3.8877487E-02 at 160iterations 1.2341248E-03 2.3147583E-02 at 170iterations 7.0613436E-04 1.3982296E-02 at 180iterations finished qdiffx linear iterations at : 21:03:32 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 7.0613436E-04 1.3982296E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 21:03:32 11.907u 0.157s 0:12.33 97.7% 0+0k 0+0io 0pf+0w