Tue Oct 11 08:20:28 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 Tue Oct 11 2011 at 08:20:28 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.6375473 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 0.6375473 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.02998 90.21590 89.46381 assigned negative charge : -414.0262 centred at (gu) : 90.27989 90.14265 89.50971 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7516 nv = 96 ne = 84 npr = 56179 no. pairs analyzed = 56179 no. exposed pairs = 3262 no. arc points = 23112 no. surface atoms = 1110 nbur = 1657 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 4262 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.3300000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4040195E-08 1.6751751E-09 midg,1,midg; midg,igrid,midg -1.3065069E-09 1.6408423E-08 1,midg,midg; igrid,midg,midg 3.5289442E-08 -2.2848626E-08 gauss-seidel spectral radius is 0.9872668 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 08:20:29 rms-change max change #iterations 0.1520739 27.61979 at 10iterations 1.5312790E-02 2.001171 at 20iterations 1.9911611E-03 0.3572121 at 30iterations 4.9132720E-04 0.1066971 at 40iterations 1.4949836E-04 3.3988953E-02 at 50iterations finished qdiffx linear iterations at : 08:20:31 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.4949836E-04 3.3988953E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:20:32 3.379u 0.157s 0:04.05 86.9% 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 Tue Oct 11 2011 at 08:20:32 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 1.912642 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 1.912642 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.08941 90.64679 88.39085 assigned negative charge : -414.0262 centred at (gu) : 90.83936 90.42749 88.52877 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23112 grid for indexing accessible points = 1.400000 m= 29209 mr = 57296 m= 4494 mr = 22098 m= 254 mr = 2934 m= 2 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 5246 time to turn everything in is 0.6100000 number of dielectric boundary points 32884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20600 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) : 0.6375473 object centre at (A) : 22.85350 6.798501 83.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0224235E-02 7.8332452E-03 midg,1,midg; midg,igrid,midg 1.4280054E-02 1.9754184E-02 1,midg,midg; igrid,midg,midg 5.2122403E-02 -4.0701404E-02 gauss-seidel spectral radius is 0.9986588 estimated iterations to convergence 216 setup time was (sec) 0.8900000 now iterating at: 08:20:33 rms-change max change #iterations 4.481845 179.2285 at 10iterations 2.102663 66.90721 at 20iterations 0.9892625 30.38037 at 30iterations 0.4672015 16.03064 at 40iterations 0.2204645 6.407430 at 50iterations 0.1039670 3.217209 at 60iterations 4.9139287E-02 1.484669 at 70iterations 2.3298705E-02 0.7117043 at 80iterations 1.1149724E-02 0.3279114 at 90iterations 5.3816559E-03 0.1626797 at 100iterations 2.6642517E-03 9.3589783E-02 at 110iterations 1.3749150E-03 5.2631378E-02 at 120iterations finished qdiffx linear iterations at : 08:20:40 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.3749150E-03 5.2631378E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 08:20:40 7.474u 0.163s 0:08.09 94.3% 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 Tue Oct 11 2011 at 08:20:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 2.868963 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): -5.066000 50.77300 ymin,ymax (A): -16.16100 29.75800 zmin,zma (A): 57.62100 109.5750 x,y,z range (A): 55.83900 45.91900 51.95401 scale (grids/A): 2.868963 object centre (A): 22.85350 6.798501 83.59800 number of atom coordinates read : 2767 total number of charged atoms : 2615 net assigned charge : 5.312018 assigned positive charge : 419.3376 centred at (gu) : 90.13400 90.96983 87.58614 assigned negative charge : -414.0262 centred at (gu) : 91.25899 90.64127 87.79303 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 188279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23112 grid for indexing accessible points = 1.400000 m= 95385 mr = 138454 m= 33918 mr = 79284 m= 8016 mr = 27760 m= 1140 mr = 6303 m= 64 mr = 808 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 17783 time to turn everything in is 1.490000 number of dielectric boundary points 74166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 20918 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) : 1.912642 object centre at (A) : 22.85350 6.798501 83.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0853341E-02 8.0640186E-03 midg,1,midg; midg,igrid,midg 0.2180232 0.2107142 1,midg,midg; igrid,midg,midg 0.6157414 -0.3201170 gauss-seidel spectral radius is 0.9992605 estimated iterations to convergence 290 setup time was (sec) 1.780000 now iterating at: 08:20:42 rms-change max change #iterations 10.35419 352.0218 at 10iterations 5.998107 135.3706 at 20iterations 3.478131 60.24442 at 30iterations 2.005999 38.38005 at 40iterations 1.155144 20.48165 at 50iterations 0.6659510 11.76652 at 60iterations 0.3827587 6.560900 at 70iterations 0.2204067 3.957790 at 80iterations 0.1268056 2.308054 at 90iterations 7.2971828E-02 1.271732 at 100iterations 4.1986816E-02 0.7408562 at 110iterations 2.4190586E-02 0.4058685 at 120iterations 1.3942576E-02 0.2535706 at 130iterations 8.0885068E-03 0.1492310 at 140iterations 4.7205351E-03 8.9784622E-02 at 150iterations 2.7945850E-03 5.2696228E-02 at 160iterations 1.7009354E-03 3.5301208E-02 at 170iterations 1.0832136E-03 2.4780273E-02 at 180iterations finished qdiffx linear iterations at : 08:20:52 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 1.0832136E-03 2.4780273E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 08:20:53 12.130u 0.172s 0:12.83 95.8% 0+0k 0+0io 0pf+0w