Wed Dec 28 11:02:55 PST 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 Wed Dec 28 2011 at 11:02:55 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.5825751 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 0.5825751 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.8744 centred at (gu) : 89.97867 90.23858 90.50111 assigned negative charge : -289.8262 centred at (gu) : 89.97916 90.33467 90.64906 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4480 nv = 96 ne = 84 npr = 40422 no. pairs analyzed = 40422 no. exposed pairs = 2408 no. arc points = 17114 no. surface atoms = 821 nbur = 1143 mkacc time = 0.1400000 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 = 1.484000 m= 202 mr = 2433 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3400000 number of dielectric boundary points 2237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 5436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6504632E-09 -8.5068885E-09 midg,1,midg; midg,igrid,midg -3.5493355E-09 -7.1240347E-09 1,midg,midg; igrid,midg,midg -5.2438223E-09 -5.2089693E-09 gauss-seidel spectral radius is 0.9847069 estimated iterations to convergence 66 setup time was (sec) 0.7900000 now iterating at: 11:02:57 rms-change max change #iterations 8.5664809E-02 16.02810 at 10iterations 6.7106616E-03 1.209953 at 20iterations 5.3561607E-04 9.9326611E-02 at 30iterations 4.0708481E-05 7.1754456E-03 at 40iterations 3.2445685E-06 5.4550171E-04 at 50iterations finished qdiffx linear iterations at : 11:03:02 total time elapsed so far: 5.780000 # loops : 50 mean,max change (kT/e) : 3.2445685E-06 5.4550171E-04 energy calculations done at 5.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.000000 DelPhi exited at 11:03:02 6.003u 0.651s 0:07.15 93.0% 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 Wed Dec 28 2011 at 11:03:02 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.747725 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 1.747725 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.8744 centred at (gu) : 89.93631 90.71593 91.50366 assigned negative charge : -289.8262 centred at (gu) : 89.93755 91.00410 91.94729 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 48823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17114 grid for indexing accessible points = 1.400000 m= 16603 mr = 33353 m= 1914 mr = 12411 m= 52 mr = 1080 m= 0 mr = 10 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 0.5500000 number of dielectric boundary points 20538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13753 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) : 0.5825751 object centre at (A) : 4.926002 0.8255005 17.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7742138E-03 -2.6833272E-02 midg,1,midg; midg,igrid,midg -1.1644171E-02 -2.2430355E-02 1,midg,midg; igrid,midg,midg -2.6919032E-02 -3.2470033E-02 gauss-seidel spectral radius is 0.9983022 estimated iterations to convergence 193 setup time was (sec) 1.000000 now iterating at: 11:03:04 rms-change max change #iterations 3.060727 163.2184 at 10iterations 1.308183 59.13194 at 20iterations 0.5622824 26.53727 at 30iterations 0.2406184 10.05757 at 40iterations 0.1035277 4.722183 at 50iterations 4.4250805E-02 1.879040 at 60iterations 1.9036800E-02 0.7922754 at 70iterations 8.1208404E-03 0.3155055 at 80iterations 3.5006108E-03 0.1509236 at 90iterations 1.4945667E-03 6.5063953E-02 at 100iterations 6.4166589E-04 2.7233124E-02 at 110iterations 2.7626017E-04 1.0695457E-02 at 120iterations finished qdiffx linear iterations at : 11:03:19 total time elapsed so far: 16.07000 # loops : 120 mean,max change (kT/e) : 2.7626017E-04 1.0695457E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.29000 DelPhi exited at 11:03:20 16.292u 0.725s 0:17.36 97.9% 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 Wed Dec 28 2011 at 11:03:20 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 2.621588 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 2.621588 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.8744 centred at (gu) : 89.90462 91.07401 92.25565 assigned negative charge : -289.8262 centred at (gu) : 89.90650 91.50613 92.92099 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 112959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17114 grid for indexing accessible points = 1.400000 m= 56026 mr = 80985 m= 17715 mr = 46167 m= 3061 mr = 14302 m= 238 mr = 2164 m= 11 mr = 134 m= 0 mr = 3 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 6558 time to turn everything in is 1.370000 number of dielectric boundary points 46255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 14105 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) : 1.747725 object centre at (A) : 4.926002 0.8255005 17.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2960146E-02 -0.3134520 midg,1,midg; midg,igrid,midg -0.1306295 -0.2648187 1,midg,midg; igrid,midg,midg -0.3259968 -0.4250079 gauss-seidel spectral radius is 0.9991432 estimated iterations to convergence 270 setup time was (sec) 1.750000 now iterating at: 11:03:22 rms-change max change #iterations 7.423827 309.9008 at 10iterations 4.130478 112.5981 at 20iterations 2.280349 60.54142 at 30iterations 1.256605 30.11630 at 40iterations 0.6914868 15.66082 at 50iterations 0.3797338 9.330849 at 60iterations 0.2085271 4.623020 at 70iterations 0.1146346 2.563950 at 80iterations 6.2893286E-02 1.452591 at 90iterations 3.4598071E-02 0.8052549 at 100iterations 1.9004032E-02 0.4468594 at 110iterations 1.0410598E-02 0.2465901 at 120iterations 5.7140389E-03 0.1465969 at 130iterations 3.1462826E-03 7.3539734E-02 at 140iterations 1.7267497E-03 3.9290428E-02 at 150iterations 9.4841182E-04 2.1442413E-02 at 160iterations 5.2072300E-04 1.1746883E-02 at 170iterations 2.8650637E-04 6.5126419E-03 at 180iterations finished qdiffx linear iterations at : 11:03:47 total time elapsed so far: 26.54000 # loops : 180 mean,max change (kT/e) : 2.8650637E-04 6.5126419E-03 energy calculations done at 26.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.76000 DelPhi exited at 11:03:48 26.760u 0.620s 0:27.96 97.9% 0+0k 0+0io 0pf+0w