Sat Oct 15 15:55:50 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 Sat Oct 15 2011 at 15:55:50 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ASN 245 has a net charge of -0.5000 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: 0.7304662 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 0.7304662 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 6.431010 assigned positive charge : 318.5141 centred at (gu) : 88.97285 88.92159 90.14918 assigned negative charge : -312.0831 centred at (gu) : 89.07597 89.02968 90.21572 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7580 nv = 96 ne = 84 npr = 41715 no. pairs analyzed = 41715 no. exposed pairs = 2516 no. arc points = 17504 no. surface atoms = 848 nbur = 1232 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 4416 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1571 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8137 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3973651E-07 3.6438493E-08 midg,1,midg; midg,igrid,midg 2.1689358E-07 1.9690301E-09 1,midg,midg; igrid,midg,midg 2.0995603E-07 5.3203553E-09 gauss-seidel spectral radius is 0.9902256 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 15:55:51 rms-change max change #iterations 0.2325573 30.03733 at 10iterations 3.1084497E-02 4.150581 at 20iterations 4.1889031E-03 0.5261078 at 30iterations 6.4824737E-04 7.7213287E-02 at 40iterations 1.3904125E-04 1.8646240E-02 at 50iterations finished qdiffx linear iterations at : 15:55:54 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.3904125E-04 1.8646240E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 15:55:54 3.360u 0.158s 0:03.85 91.1% 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 Sat Oct 15 2011 at 15:55:54 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ASN 245 has a net charge of -0.5000 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: 2.191399 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 2.191399 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 6.431010 assigned positive charge : 318.5141 centred at (gu) : 86.91865 86.76485 90.44759 assigned negative charge : -312.0831 centred at (gu) : 87.22781 87.08928 90.64718 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17504 grid for indexing accessible points = 1.400000 m= 33118 mr = 57312 m= 6598 mr = 25436 m= 624 mr = 4464 m= 22 mr = 311 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15486 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) : 0.7304662 object centre at (A) : 10.53000 1.444500 7.559000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4365956E-02 2.6175868E-02 midg,1,midg; midg,igrid,midg 4.7290161E-02 -4.2697001E-02 1,midg,midg; igrid,midg,midg 0.1014216 4.8302144E-02 gauss-seidel spectral radius is 0.9988938 estimated iterations to convergence 238 setup time was (sec) 0.9300000 now iterating at: 15:55:55 rms-change max change #iterations 4.909198 227.4417 at 10iterations 2.475914 80.60633 at 20iterations 1.254697 38.62969 at 30iterations 0.6333593 18.52246 at 40iterations 0.3212568 9.183136 at 50iterations 0.1628068 4.816212 at 60iterations 8.2237236E-02 2.272049 at 70iterations 4.1732367E-02 1.244686 at 80iterations 2.1098731E-02 0.5830812 at 90iterations 1.0792952E-02 0.3312082 at 100iterations 5.5390075E-03 0.1792808 at 110iterations 2.8557591E-03 8.1680298E-02 at 120iterations finished qdiffx linear iterations at : 15:56:02 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.8557591E-03 8.1680298E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 15:56:02 7.749u 0.165s 0:08.21 96.2% 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 15 2011 at 15:56:02 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2080 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ASN 245 has a net charge of -0.5000 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: 3.287098 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 3.287098 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1946 net assigned charge : 6.431010 assigned positive charge : 318.5141 centred at (gu) : 85.37794 85.14722 90.67149 assigned negative charge : -312.0831 centred at (gu) : 85.84176 85.63384 90.97079 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 184980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17504 grid for indexing accessible points = 1.400000 m= 102314 mr = 137823 m= 42440 mr = 85796 m= 12566 mr = 35174 m= 2544 mr = 9782 m= 352 mr = 1824 m= 20 mr = 234 m= 0 mr = 7 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 74576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15568 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) : 2.191399 object centre at (A) : 10.53000 1.444500 7.559000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1171482 0.2408699 midg,1,midg; midg,igrid,midg 0.4174024 -0.5030147 1,midg,midg; igrid,midg,midg 0.8044304 0.2945488 gauss-seidel spectral radius is 0.9993139 estimated iterations to convergence 301 setup time was (sec) 2.290000 now iterating at: 15:56:05 rms-change max change #iterations 10.74430 335.4729 at 10iterations 6.376478 191.3703 at 20iterations 3.783884 72.35365 at 30iterations 2.244571 51.09484 at 40iterations 1.328267 22.46147 at 50iterations 0.7848366 19.58460 at 60iterations 0.4632984 8.301663 at 70iterations 0.2734154 4.690353 at 80iterations 0.1612209 2.602888 at 90iterations 9.5120177E-02 1.778051 at 100iterations 5.6389946E-02 0.9248714 at 110iterations 3.3380497E-02 0.5683060 at 120iterations 1.9829681E-02 0.3487358 at 130iterations 1.1964084E-02 0.2133875 at 140iterations 7.3455288E-03 0.1291409 at 150iterations 4.6579624E-03 7.7564240E-02 at 160iterations 3.0764942E-03 5.4389954E-02 at 170iterations 2.1554288E-03 3.4652710E-02 at 180iterations finished qdiffx linear iterations at : 15:56:16 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 2.1554288E-03 3.4652710E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 15:56:16 13.060u 0.192s 0:13.57 97.6% 0+0k 0+0io 0pf+0w