Tue Oct 11 06:04:51 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 Tue Oct 11 2011 at 06:04:51 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 = 2061 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: 0.7419140 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 0.7419140 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 90.11401 89.60865 90.94123 assigned negative charge : -306.0842 centred at (gu) : 90.05478 89.51686 90.83194 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7928 nv = 96 ne = 84 npr = 41244 no. pairs analyzed = 41244 no. exposed pairs = 2501 no. arc points = 17116 no. surface atoms = 846 nbur = 1215 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 607 mr = 4722 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2900000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1501 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0675883E-09 2.7151967E-07 midg,1,midg; midg,igrid,midg 2.6479746E-08 1.9584131E-07 1,midg,midg; igrid,midg,midg 5.7369640E-08 1.8186452E-07 gauss-seidel spectral radius is 0.9905218 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 06:04:52 rms-change max change #iterations 0.2437142 33.88262 at 10iterations 3.3600565E-02 4.583069 at 20iterations 4.6848091E-03 0.6094284 at 30iterations 7.6219224E-04 8.2470894E-02 at 40iterations 1.7334295E-04 1.9449234E-02 at 50iterations finished qdiffx linear iterations at : 06:04:54 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.7334295E-04 1.9449234E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 06:04:55 3.636u 0.212s 0:04.43 86.6% 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 Tue Oct 11 2011 at 06:04:55 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 = 2061 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: 2.225742 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 2.225742 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 90.34214 88.82603 92.82367 assigned negative charge : -306.0842 centred at (gu) : 90.16435 88.55072 92.49592 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17116 grid for indexing accessible points = 1.400000 m= 35614 mr = 59752 m= 7733 mr = 27865 m= 812 mr = 5340 m= 37 mr = 477 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 219 time to turn everything in is 0.7200000 number of dielectric boundary points 33750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15385 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) : 0.7419140 object centre at (A) : 5.901000 9.608500 14.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3632466E-02 4.4125102E-02 midg,1,midg; midg,igrid,midg 3.5298988E-02 3.2748923E-02 1,midg,midg; igrid,midg,midg 5.7128593E-02 3.5516266E-02 gauss-seidel spectral radius is 0.9989206 estimated iterations to convergence 241 setup time was (sec) 1.020000 now iterating at: 06:04:57 rms-change max change #iterations 4.974566 207.7976 at 10iterations 2.527964 77.21341 at 20iterations 1.290395 36.68266 at 30iterations 0.6576479 20.56530 at 40iterations 0.3351843 9.344164 at 50iterations 0.1714317 5.204926 at 60iterations 8.7560058E-02 2.431763 at 70iterations 4.4720255E-02 1.264772 at 80iterations 2.2922819E-02 0.6667786 at 90iterations 1.1812250E-02 0.3545589 at 100iterations 6.1004637E-03 0.1678810 at 110iterations 3.1940811E-03 9.7419739E-02 at 120iterations finished qdiffx linear iterations at : 06:05:06 total time elapsed so far: 10.76000 # loops : 120 mean,max change (kT/e) : 3.1940811E-03 9.7419739E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 06:05:07 10.962u 0.262s 0:11.67 96.1% 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 Tue Oct 11 2011 at 06:05:07 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 = 2061 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: 3.338613 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): -18.09100 29.89300 ymin,ymax (A): -11.78100 30.99800 zmin,zma (A): -8.529000 38.19800 x,y,z range (A): 47.98400 42.77900 46.72700 scale (grids/A): 3.338613 object centre (A): 5.901000 9.608500 14.83450 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 90.51306 88.23903 94.23575 assigned negative charge : -306.0842 centred at (gu) : 90.24652 87.82607 93.74390 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 190834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17116 grid for indexing accessible points = 1.400000 m= 108322 mr = 143118 m= 47584 mr = 91533 m= 14999 mr = 40136 m= 3400 mr = 11977 m= 537 mr = 2537 m= 32 mr = 373 m= 0 mr = 13 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 722 time to turn everything in is 2.080000 number of dielectric boundary points 76021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 15464 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) : 2.225742 object centre at (A) : 5.901000 9.608500 14.83450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4745799 0.4359695 midg,1,midg; midg,igrid,midg 0.2889283 0.1893812 1,midg,midg; igrid,midg,midg 0.3512895 0.1372424 gauss-seidel spectral radius is 0.9993200 estimated iterations to convergence 303 setup time was (sec) 2.380000 now iterating at: 06:05:10 rms-change max change #iterations 10.82119 305.8107 at 10iterations 6.474578 139.7727 at 20iterations 3.859718 74.52835 at 30iterations 2.301912 39.10699 at 40iterations 1.368324 25.43780 at 50iterations 0.8116274 13.63678 at 60iterations 0.4813562 8.819625 at 70iterations 0.2857214 4.818199 at 80iterations 0.1690156 2.776209 at 90iterations 9.9948384E-02 1.582594 at 100iterations 5.9306554E-02 1.004556 at 110iterations 3.5222687E-02 0.5611115 at 120iterations 2.1072928E-02 0.3978806 at 130iterations 1.2773078E-02 0.2105370 at 140iterations 7.9156030E-03 0.1355858 at 150iterations 5.0796275E-03 9.0425491E-02 at 160iterations 3.4295272E-03 5.7884216E-02 at 170iterations 2.4656402E-03 4.4414520E-02 at 180iterations finished qdiffx linear iterations at : 06:05:20 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.4656402E-03 4.4414520E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 06:05:21 13.233u 0.165s 0:13.84 96.7% 0+0k 0+0io 0pf+0w