Sat Oct 8 14:26:07 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 14:26:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6397010 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 0.6397010 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 7.1674585E-06 assigned positive charge : 455.7956 centred at (gu) : 88.75071 89.96299 91.48853 assigned negative charge : -455.7963 centred at (gu) : 88.74155 89.86685 91.39697 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8165 nv = 96 ne = 84 npr = 64361 no. pairs analyzed = 64361 no. exposed pairs = 3430 no. arc points = 24161 no. surface atoms = 1172 nbur = 1868 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4760 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2337 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1963903E-09 1.6798818E-08 midg,1,midg; midg,igrid,midg -1.3434525E-08 1.2606683E-08 1,midg,midg; igrid,midg,midg -1.8598112E-09 8.1339169E-10 gauss-seidel spectral radius is 0.9873707 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 14:26:08 rms-change max change #iterations 0.1587641 20.36028 at 10iterations 1.6064636E-02 2.108270 at 20iterations 1.6298811E-03 0.2169895 at 30iterations 1.8096076E-04 2.1817446E-02 at 40iterations 2.4255100E-05 3.3187866E-03 at 50iterations finished qdiffx linear iterations at : 14:26:11 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 2.4255100E-05 3.3187866E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 14:26:12 3.717u 0.218s 0:04.23 92.6% 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 Sat Oct 8 2011 at 14:26:12 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 = 3040 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.919103 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 1.919103 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 7.1674585E-06 assigned positive charge : 455.7956 centred at (gu) : 86.25127 89.88835 94.46484 assigned negative charge : -455.7963 centred at (gu) : 86.22466 89.60028 94.19078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 32371 mr = 64486 m= 4721 mr = 24366 m= 281 mr = 2868 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.4400000 number of dielectric boundary points 34883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 22797 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) : 0.6397010 object centre at (A) : 15.36850 -0.3975000 20.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2857847E-02 2.4109108E-02 midg,1,midg; midg,igrid,midg 8.3932269E-04 2.3475846E-02 1,midg,midg; igrid,midg,midg -3.3781677E-02 9.9119116E-03 gauss-seidel spectral radius is 0.9986890 estimated iterations to convergence 219 setup time was (sec) 0.6800000 now iterating at: 14:26:13 rms-change max change #iterations 4.716041 274.1958 at 10iterations 2.255607 71.96307 at 20iterations 1.073168 31.15340 at 30iterations 0.5098605 13.70923 at 40iterations 0.2435406 6.991261 at 50iterations 0.1161271 3.615084 at 60iterations 5.5103738E-02 1.621889 at 70iterations 2.6278554E-02 0.7202049 at 80iterations 1.2488514E-02 0.3465271 at 90iterations 5.9575508E-03 0.1706543 at 100iterations 2.8408619E-03 8.0173492E-02 at 110iterations 1.3576049E-03 3.8303375E-02 at 120iterations finished qdiffx linear iterations at : 14:26:20 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 1.3576049E-03 3.8303375E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.630000 DelPhi exited at 14:26:21 8.630u 0.251s 0:09.21 96.4% 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 Sat Oct 8 2011 at 14:26:21 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 = 3040 !!! WARNING: NAP 500 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.878654 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 2.878654 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 7.1674585E-06 assigned positive charge : 455.7956 centred at (gu) : 84.37676 89.83242 96.69707 assigned negative charge : -455.7963 centred at (gu) : 84.33688 89.40040 96.28611 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 206868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 105654 mr = 155497 m= 37027 mr = 88025 m= 8424 mr = 29952 m= 1223 mr = 6274 m= 65 mr = 795 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 444 time to turn everything in is 1.170000 number of dielectric boundary points 78689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 23144 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) : 1.919103 object centre at (A) : 15.36850 -0.3975000 20.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7800575E-02 0.3493488 midg,1,midg; midg,igrid,midg 9.7523388E-03 0.2536875 1,midg,midg; igrid,midg,midg -0.4829319 0.1520791 gauss-seidel spectral radius is 0.9992762 estimated iterations to convergence 293 setup time was (sec) 1.440000 now iterating at: 14:26:23 rms-change max change #iterations 10.98752 400.9613 at 10iterations 6.466161 131.7863 at 20iterations 3.783572 67.66974 at 30iterations 2.207789 43.60101 at 40iterations 1.283459 25.53512 at 50iterations 0.7472100 14.91313 at 60iterations 0.4339651 7.256272 at 70iterations 0.2516457 4.501060 at 80iterations 0.1460179 2.761353 at 90iterations 8.4625609E-02 1.396683 at 100iterations 4.9022630E-02 0.7646813 at 110iterations 2.8358437E-02 0.4805331 at 120iterations 1.6474398E-02 0.2642329 at 130iterations 9.5541924E-03 0.1577072 at 140iterations 5.5390247E-03 8.8726044E-02 at 150iterations 3.2136589E-03 5.5355072E-02 at 160iterations 1.8694323E-03 3.3599854E-02 at 170iterations 1.0937551E-03 1.9805908E-02 at 180iterations finished qdiffx linear iterations at : 14:26:35 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.0937551E-03 1.9805908E-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) 14.07000 DelPhi exited at 14:26:36 14.075u 0.267s 0:14.67 97.6% 0+0k 0+0io 0pf+0w