Mon Oct 10 14:06:10 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 14:06:11 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5004358 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 0.5004358 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719568 assigned positive charge : 823.8615 centred at (gu) : 89.46947 89.06776 89.19949 assigned negative charge : -824.6392 centred at (gu) : 89.38422 89.00368 89.28737 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8350 nv = 96 ne = 84 npr = 106392 no. pairs analyzed = 106392 no. exposed pairs = 6829 no. arc points = 46271 no. surface atoms = 2297 nbur = 3042 mkacc time = 0.2500000 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 = 1.708000 m= 304 mr = 4328 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4447 ## 664 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 11372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0017127E-10 -1.4225060E-10 midg,1,midg; midg,igrid,midg -1.6787584E-10 9.0003609E-11 1,midg,midg; igrid,midg,midg -1.9830289E-10 1.3482591E-10 gauss-seidel spectral radius is 0.9796220 estimated iterations to convergence 58 setup time was (sec) 0.8300000 now iterating at: 14:06:12 rms-change max change #iterations 6.6794343E-02 11.19699 at 10iterations 4.9876161E-03 0.8739395 at 20iterations 1.6381000E-03 0.2484570 at 30iterations 7.6050760E-04 0.1111717 at 40iterations 3.6656254E-04 4.9238205E-02 at 50iterations finished qdiffx linear iterations at : 14:06:14 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 3.6656254E-04 4.9238205E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 14:06:15 3.827u 0.177s 0:04.41 90.4% 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 14:06:15 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.501307 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 1.501307 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719568 assigned positive charge : 823.8615 centred at (gu) : 88.40708 87.20213 87.59696 assigned negative charge : -824.6392 centred at (gu) : 88.15283 87.01060 87.86247 start vw surface at 0.2400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 94190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46271 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 29302 mr = 64456 m= 2599 mr = 20143 m= 36 mr = 1157 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.7700000 number of dielectric boundary points 40371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 518 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 38531 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) : 0.5004358 object centre at (A) : 41.88650 3.048501 28.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8563591E-03 -1.6162412E-02 midg,1,midg; midg,igrid,midg -1.9978266E-03 1.2175061E-02 1,midg,midg; igrid,midg,midg -1.3859790E-03 2.6988873E-04 gauss-seidel spectral radius is 0.9980853 estimated iterations to convergence 182 setup time was (sec) 1.150000 now iterating at: 14:06:16 rms-change max change #iterations 3.967338 175.6925 at 10iterations 1.606360 59.96351 at 20iterations 0.6522923 21.65337 at 30iterations 0.2661602 9.123680 at 40iterations 0.1089988 3.347301 at 50iterations 4.4482503E-02 1.415667 at 60iterations 1.8452991E-02 0.5439148 at 70iterations 7.9477346E-03 0.2586021 at 80iterations 3.7288573E-03 0.1258698 at 90iterations 2.0354274E-03 6.2240601E-02 at 100iterations 1.3219070E-03 4.1988373E-02 at 110iterations 9.4870193E-04 2.7719498E-02 at 120iterations finished qdiffx linear iterations at : 14:06:24 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 9.4870193E-04 2.7719498E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 14:06:24 8.828u 0.216s 0:09.43 95.7% 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 14:06:24 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.251961 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 2.251961 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719568 assigned positive charge : 823.8615 centred at (gu) : 87.61009 85.80305 86.39513 assigned negative charge : -824.6392 centred at (gu) : 87.22914 85.51582 86.79372 start vw surface at 0.2700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 219199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46271 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102170 mr = 158086 m= 27845 mr = 80579 m= 3648 mr = 20903 m= 160 mr = 2274 m= 0 mr = 27 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 1.750000 number of dielectric boundary points 91153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 41163 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) : 1.501307 object centre at (A) : 41.88650 3.048501 28.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1214672E-02 -0.3326083 midg,1,midg; midg,igrid,midg -1.3992081E-04 0.1420299 1,midg,midg; igrid,midg,midg -7.9577020E-04 1.9305559E-03 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 274 setup time was (sec) 2.090000 now iterating at: 14:06:27 rms-change max change #iterations 10.95940 287.6591 at 10iterations 6.335630 144.6802 at 20iterations 3.632640 87.00705 at 30iterations 2.069056 43.64460 at 40iterations 1.173122 24.68775 at 50iterations 0.6622584 13.82082 at 60iterations 0.3720694 6.782001 at 70iterations 0.2099416 3.552353 at 80iterations 0.1176915 2.135996 at 90iterations 6.6075593E-02 1.211647 at 100iterations 3.6970358E-02 0.6962872 at 110iterations 2.0774974E-02 0.3813219 at 120iterations 1.1722210E-02 0.2222786 at 130iterations 6.6667148E-03 0.1188622 at 140iterations 3.8544771E-03 6.9636345E-02 at 150iterations 2.3190298E-03 5.1609039E-02 at 160iterations 1.4842872E-03 2.6749134E-02 at 170iterations 1.0263768E-03 1.8705368E-02 at 180iterations finished qdiffx linear iterations at : 14:06:39 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.0263768E-03 1.8705368E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 14:06:39 14.131u 0.193s 0:14.65 97.7% 0+0k 0+0io 0pf+0w