Mon Oct 10 14:03:08 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+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 Mon Oct 10 2011 at 14:03:09 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3588 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1010 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5960254 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): 12.83100 72.26500 ymin,ymax (A): 50.97800 109.4230 zmin,zma (A): -4.139000 55.59000 x,y,z range (A): 59.43400 58.44501 59.72900 scale (grids/A): 0.5960254 object centre (A): 42.54800 80.20050 25.72550 number of atom coordinates read : 3588 total number of charged atoms : 3008 net assigned charge : 16.80602 assigned positive charge : 468.9292 centred at (gu) : 89.75797 90.17294 91.79670 assigned negative charge : -452.1245 centred at (gu) : 89.73222 90.28844 91.87891 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8562 nv = 96 ne = 84 npr = 73333 no. pairs analyzed = 73333 no. exposed pairs = 5073 no. arc points = 35599 no. surface atoms = 1691 nbur = 1897 mkacc time = 0.1200000 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= 451 mr = 4195 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2600000 number of dielectric boundary points 4788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2937 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3187628E-09 4.7846385E-09 midg,1,midg; midg,igrid,midg 1.0231849E-08 2.0649045E-09 1,midg,midg; igrid,midg,midg 5.7040186E-09 6.9520385E-09 gauss-seidel spectral radius is 0.9855319 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:03:09 rms-change max change #iterations 0.1207349 19.19850 at 10iterations 1.0032794E-02 1.526871 at 20iterations 9.4391569E-04 0.1439157 at 30iterations 1.2699841E-04 1.7269135E-02 at 40iterations 2.8600121E-05 4.3311119E-03 at 50iterations finished qdiffx linear iterations at : 14:03:12 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.8600121E-05 4.3311119E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:03:13 3.454u 0.169s 0:04.25 84.9% 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 Mon Oct 10 2011 at 14:03:13 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3588 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1010 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.788076 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): 12.83100 72.26500 ymin,ymax (A): 50.97800 109.4230 zmin,zma (A): -4.139000 55.59000 x,y,z range (A): 59.43400 58.44501 59.72900 scale (grids/A): 1.788076 object centre (A): 42.54800 80.20050 25.72550 number of atom coordinates read : 3588 total number of charged atoms : 3008 net assigned charge : 16.80602 assigned positive charge : 468.9292 centred at (gu) : 89.27306 90.51803 95.38986 assigned negative charge : -452.1245 centred at (gu) : 89.19630 90.86496 95.63643 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 92285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35599 grid for indexing accessible points = 1.400000 m= 31001 mr = 60002 m= 4442 mr = 21213 m= 231 mr = 2436 m= 5 mr = 46 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 44268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 23450 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) : 0.5960254 object centre at (A) : 42.54800 80.20050 25.72550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3829059E-02 3.3173338E-02 midg,1,midg; midg,igrid,midg 3.5523359E-02 2.5183354E-02 1,midg,midg; igrid,midg,midg 4.0504251E-02 4.2923089E-02 gauss-seidel spectral radius is 0.9985759 estimated iterations to convergence 210 setup time was (sec) 0.6800000 now iterating at: 14:03:14 rms-change max change #iterations 4.212383 196.6929 at 10iterations 1.934355 63.54334 at 20iterations 0.8872514 28.50918 at 30iterations 0.4097592 12.21824 at 40iterations 0.1887060 5.689199 at 50iterations 8.6633116E-02 2.968801 at 60iterations 3.9924096E-02 1.199556 at 70iterations 1.8400246E-02 0.5645312 at 80iterations 8.4720803E-03 0.2431149 at 90iterations 3.9093695E-03 0.1222839 at 100iterations 1.8024123E-03 5.5809140E-02 at 110iterations 8.3315955E-04 2.5759697E-02 at 120iterations finished qdiffx linear iterations at : 14:03:21 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 8.3315955E-04 2.5759697E-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 14:03:22 8.133u 0.195s 0:08.93 93.1% 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 Mon Oct 10 2011 at 14:03:22 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3588 !!! WARNING: GLM 151 has a net charge of -0.0940 !!! WARNING: MG1 1010 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.682114 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): 12.83100 72.26500 ymin,ymax (A): 50.97800 109.4230 zmin,zma (A): -4.139000 55.59000 x,y,z range (A): 59.43400 58.44501 59.72900 scale (grids/A): 2.682114 object centre (A): 42.54800 80.20050 25.72550 number of atom coordinates read : 3588 total number of charged atoms : 3008 net assigned charge : 16.80602 assigned positive charge : 468.9292 centred at (gu) : 88.90948 90.77683 98.08452 assigned negative charge : -452.1245 centred at (gu) : 88.79453 91.29733 98.45444 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 213617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35599 grid for indexing accessible points = 1.400000 m= 101456 mr = 147282 m= 34207 mr = 78993 m= 7646 mr = 26112 m= 954 mr = 5339 m= 33 mr = 532 m= 0 mr = 8 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 99647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 24061 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) : 1.788076 object centre at (A) : 42.54800 80.20050 25.72550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3642859 0.3160688 midg,1,midg; midg,igrid,midg 0.3640543 0.5304604 1,midg,midg; igrid,midg,midg 0.2102789 0.5208611 gauss-seidel spectral radius is 0.9992815 estimated iterations to convergence 294 setup time was (sec) 1.370000 now iterating at: 14:03:23 rms-change max change #iterations 10.25331 334.6236 at 10iterations 6.089274 126.5389 at 20iterations 3.594720 82.11157 at 30iterations 2.107302 43.83628 at 40iterations 1.231923 25.42840 at 50iterations 0.7199152 14.13175 at 60iterations 0.4187005 7.266542 at 70iterations 0.2434918 4.402450 at 80iterations 0.1416523 2.625549 at 90iterations 8.2229868E-02 1.595611 at 100iterations 4.7669590E-02 0.8181543 at 110iterations 2.7752716E-02 0.5055885 at 120iterations 1.6068310E-02 0.2760468 at 130iterations 9.3316277E-03 0.1636009 at 140iterations 5.3985706E-03 9.3960047E-02 at 150iterations 3.1342146E-03 5.3530693E-02 at 160iterations 1.8202171E-03 3.1599045E-02 at 170iterations 1.0562227E-03 1.6952515E-02 at 180iterations finished qdiffx linear iterations at : 14:03:35 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.0562227E-03 1.6952515E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 14:03:36 13.110u 0.219s 0:14.25 93.4% 0+0k 0+0io 0pf+0w