Sat Oct 8 14:40:33 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 14:40:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 0.6405066 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): -11.90200 43.67900 ymin,ymax (A): -22.96900 18.00400 zmin,zma (A): -7.404000 47.68900 x,y,z range (A): 55.58100 40.97300 55.09300 scale (grids/A): 0.6405066 object centre (A): 15.88850 -2.482500 20.14250 number of atom coordinates read : 2511 total number of charged atoms : 2370 net assigned charge : -1.999989 assigned positive charge : 368.2614 centred at (gu) : 89.35990 89.84525 91.23500 assigned negative charge : -370.2618 centred at (gu) : 89.45404 89.85262 91.13863 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 52915 no. pairs analyzed = 52915 no. exposed pairs = 2927 no. arc points = 20713 no. surface atoms = 1005 nbur = 1506 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3898 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1977 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8301 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0855874E-08 1.0000579E-08 midg,1,midg; midg,igrid,midg -2.4115514E-09 -3.8704533E-09 1,midg,midg; igrid,midg,midg 8.4627709E-09 -1.2100840E-08 gauss-seidel spectral radius is 0.9873605 estimated iterations to convergence 73 setup time was (sec) 0.7500000 now iterating at: 14:40:36 rms-change max change #iterations 0.1462276 26.98967 at 10iterations 1.4358056E-02 2.168739 at 20iterations 1.4504433E-03 0.2019563 at 30iterations 1.4740127E-04 1.9508362E-02 at 40iterations 1.4738953E-05 2.3021698E-03 at 50iterations finished qdiffx linear iterations at : 14:40:43 total time elapsed so far: 7.770000 # loops : 50 mean,max change (kT/e) : 1.4738953E-05 2.3021698E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 14:40:43 7.947u 0.677s 0:10.52 81.8% 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 Sat Oct 8 2011 at 14:40:43 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 1.921520 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): -11.90200 43.67900 ymin,ymax (A): -22.96900 18.00400 zmin,zma (A): -7.404000 47.68900 x,y,z range (A): 55.58100 40.97300 55.09300 scale (grids/A): 1.921520 object centre (A): 15.88850 -2.482500 20.14250 number of atom coordinates read : 2511 total number of charged atoms : 2370 net assigned charge : -1.999989 assigned positive charge : 368.2614 centred at (gu) : 88.07910 89.53543 93.70482 assigned negative charge : -370.2618 centred at (gu) : 88.36207 89.55772 93.41580 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20713 grid for indexing accessible points = 1.400000 m= 26321 mr = 53598 m= 3729 mr = 19360 m= 213 mr = 2276 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 30142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 18672 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) : 0.6405066 object centre at (A) : 15.88850 -2.482500 20.14250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4284501E-02 2.7664048E-03 midg,1,midg; midg,igrid,midg 3.4157393E-04 -9.2246914E-03 1,midg,midg; igrid,midg,midg 5.1019810E-02 -1.6451782E-02 gauss-seidel spectral radius is 0.9986461 estimated iterations to convergence 215 setup time was (sec) 1.160000 now iterating at: 14:40:47 rms-change max change #iterations 4.207798 216.2318 at 10iterations 1.981077 68.63461 at 20iterations 0.9271998 30.13917 at 30iterations 0.4377065 14.22614 at 40iterations 0.2049336 6.289948 at 50iterations 9.6411251E-02 3.300920 at 60iterations 4.5226708E-02 1.560715 at 70iterations 2.1277387E-02 0.6722450 at 80iterations 1.0002332E-02 0.3023472 at 90iterations 4.7221584E-03 0.1459782 at 100iterations 2.2197166E-03 7.5689793E-02 at 110iterations 1.0476629E-03 3.2172322E-02 at 120iterations finished qdiffx linear iterations at : 14:41:03 total time elapsed so far: 16.85000 # loops : 120 mean,max change (kT/e) : 1.0476629E-03 3.2172322E-02 energy calculations done at 16.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.04000 DelPhi exited at 14:41:04 17.047u 0.757s 0:20.63 86.2% 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 14:41:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 2.882280 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): -11.90200 43.67900 ymin,ymax (A): -22.96900 18.00400 zmin,zma (A): -7.404000 47.68900 x,y,z range (A): 55.58100 40.97300 55.09300 scale (grids/A): 2.882280 object centre (A): 15.88850 -2.482500 20.14250 number of atom coordinates read : 2511 total number of charged atoms : 2370 net assigned charge : -1.999989 assigned positive charge : 368.2614 centred at (gu) : 87.11871 89.30320 95.55719 assigned negative charge : -370.2618 centred at (gu) : 87.54314 89.33651 95.12372 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20713 grid for indexing accessible points = 1.400000 m= 86599 mr = 129544 m= 29311 mr = 71358 m= 6529 mr = 23325 m= 921 mr = 4729 m= 49 mr = 580 m= 0 mr = 12 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 67955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 18960 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) : 1.921520 object centre at (A) : 15.88850 -2.482500 20.14250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1175920 1.9136282E-02 midg,1,midg; midg,igrid,midg 1.1013343E-02 -8.7173767E-02 1,midg,midg; igrid,midg,midg 0.9901435 -0.2150525 gauss-seidel spectral radius is 0.9992560 estimated iterations to convergence 289 setup time was (sec) 2.320000 now iterating at: 14:41:07 rms-change max change #iterations 9.862907 412.2415 at 10iterations 5.770562 132.0177 at 20iterations 3.358427 69.39952 at 30iterations 1.946579 38.60493 at 40iterations 1.124338 22.53347 at 50iterations 0.6500034 16.32130 at 60iterations 0.3747240 8.228704 at 70iterations 0.2159728 3.976828 at 80iterations 0.1242427 2.220955 at 90iterations 7.1769603E-02 1.347021 at 100iterations 4.1204419E-02 0.7690430 at 110iterations 2.3679659E-02 0.4145794 at 120iterations 1.3620717E-02 0.2363205 at 130iterations 7.8195119E-03 0.1410713 at 140iterations 4.4921101E-03 7.8710556E-02 at 150iterations 2.5803335E-03 4.5690536E-02 at 160iterations 1.4830920E-03 2.5699615E-02 at 170iterations 8.5232547E-04 1.5079886E-02 at 180iterations finished qdiffx linear iterations at : 14:41:34 total time elapsed so far: 29.14000 # loops : 180 mean,max change (kT/e) : 8.5232547E-04 1.5079886E-02 energy calculations done at 29.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.31000 DelPhi exited at 14:41:34 29.318u 0.735s 0:30.52 98.4% 0+0k 0+0io 0pf+0w