Dear Users,
Thx for suggestions
Actually I have made some libraries for Calcium and phosphate which has
sucessfully been done. Now what I direly need is to address the pentosidine
ring in my pdb. There are two residues like 359 and 360 in the lowest
portion of pdb. I tried them to add as HETATM. Things ultimately went well
with xleap but parameter file was not saved. OPT is actually the name given
by me in library making but this is not present in parm99.dat like CO atom
type for Calcium. Should I add OPT in parm99.dat manually or what?
Following is pdb information near the end
HETATM 1870 OPT PEN 359 26.126 24.635 37.223
TER 1871 PEN 359
HETATM 1872 OPT PEN 359 24.028 23.725 37.226
TER 1873 PEN 359
HETATM 1874 OPT PEN 359 19.472 28.715 37.541
TER 1875 PEN 359
HETATM 1876 OPT PEN 359 17.227 30.111 37.582
TER 1877 PEN 359
HETATM 1878 OPT PEN 359 17.216 27.839 37.662
TER 1879 PEN 359
HETATM 1880 OPT PEN 359 24.788 27.047 36.664
TER 1881 PEN 359
HETATM 1882 OPT PEN 359 15.998 29.774 37.731
TER 1883 PEN 359
HETATM 1884 OPT PEN 359 21.747 27.440 37.542
TER 1885 PEN 359
HETATM 1886 OPT PEN 359 22.490 26.067 37.337
TER 1887 PEN 359
HETATM 1888 OPT PEN 359 20.163 27.400 37.448
TER 1889 PEN 359
HETATM 1890 OPT PEN 359 15.940 28.376 37.822
TER 1891 PEN 359
HETATM 1892 OPT PEN 359 13.546 29.849 37.888
TER 1893 PEN 359
HETATM 1894 OPT PEN 359 24.077 26.098 37.496
TER 1895 PEN 359
HETATM 1896 OPT PEN 359 18.007 28.837 37.583
TER 1897 PEN 359
HETATM 1898 OPT PEN 359 14.783 27.724 37.809
TER 1899 PEN 359
HETATM 1900 OPT PEN 359 13.530 28.523 37.800
TER 1901 PEN 359
HETATM 1902 OPT PEN 359 24.723 24.740 37.290
TER 1903 PEN 359
HETATM 1904 OPT PEN 359 21.976 28.047 36.942
TER 1905 PEN 359
HETATM 1906 OPT PEN 359 22.223 28.268 37.803
TER 1907 PEN 359
HETATM 1908 OPT PEN 359 22.070 25.339 37.978
TER 1909 PEN 359
HETATM 1910 OPT PEN 359 22.263 25.679 36.387
TER 1911 PEN 359
HETATM 1912 OPT PEN 359 19.693 26.596 37.368
TER 1913 PEN 359
HETATM 1914 OPT PEN 359 19.963 26.872 38.304
TER 1915 PEN 359
HETATM 1916 OPT PEN 359 24.324 26.430 38.516
TER 1917 PEN 359
HETATM 1918 OPT PEN 359 20.021 29.540 37.508
TER 1919 PEN 359
HETATM 1920 OPT PEN 359 14.757 26.637 37.764
TER 1921 PEN 359
HETATM 1922 OPT PEN 359 12.571 28.004 37.784
TER 1923 PEN 359
HETATM 1924 OPT PEN 359 24.455 28.006 36.865
TER 1925 PEN 359
HETATM 1926 OPT PEN 359 25.798 27.009 36.839
TER 1927 PEN 359
HETATM 1928 OPT PEN 359 26.389 23.685 37.102
TER 1929 PEN 359
HETATM 1930 OPT PEN 359 12.882 30.712 37.811
TER 1931 PEN 359
HETATM 1932 OPT PEN 360 25.994 10.885 35.877
TER 1933 PEN 360
HETATM 1934 OPT PEN 360 23.896 9.994 36.003
TER 1935 PEN 360
HETATM 1936 OPT PEN 360 19.378 15.013 35.768
TER 1937 PEN 360
HETATM 1938 OPT PEN 360 17.152 16.439 35.829
TER 1939 PEN 360
HETATM 1940 OPT PEN 360 17.110 14.157 35.861
TER 1941 PEN 360
HETATM 1942 OPT PEN 360 24.759 13.418 35.798
TER 1943 PEN 360
HETATM 1944 OPT PEN 360 15.907 16.112 35.762
TER 1945 PEN 360
HETATM 1946 OPT PEN 360 21.640 13.748 35.839
TER 1947 PEN 360
HETATM 1948 OPT PEN 360 22.363 12.340 35.786
TER 1949 PEN 360
HETATM 1950 OPT PEN 360 20.046 13.671 35.745
TER 1951 PEN 360
HETATM 1952 OPT PEN 360 15.836 14.714 35.940
TER 1953 PEN 360
HETATM 1954 OPT PEN 360 13.462 16.222 35.972
TER 1955 PEN 360
HETATM 1956 OPT PEN 360 23.936 12.340 35.787
TER 1957 PEN 360
HETATM 1958 OPT PEN 360 17.915 15.151 35.826
TER 1959 PEN 360
HETATM 1960 OPT PEN 360 14.672 14.075 35.965
TER 1961 PEN 360
HETATM 1962 OPT PEN 360 13.429 14.888 36.008
TER 1963 PEN 360
HETATM 1964 OPT PEN 360 24.595 11.007 35.953
TER 1965 PEN 360
HETATM 1966 OPT PEN 360 21.877 14.146 36.813
TER 1967 PEN 360
HETATM 1968 OPT PEN 360 22.035 14.457 35.161
TER 1969 PEN 360
HETATM 1970 OPT PEN 360 21.925 11.654 36.434
TER 1971 PEN 360
HETATM 1972 OPT PEN 360 22.116 11.864 34.852
TER 1973 PEN 360
HETATM 1974 OPT PEN 360 19.657 13.049 36.525
TER 1975 PEN 360
HETATM 1976 OPT PEN 360 19.800 13.194 34.799
TER 1977 PEN 360
HETATM 1978 OPT PEN 360 24.097 12.522 34.610
TER 1979 PEN 360
HETATM 1980 OPT PEN 360 19.940 15.830 35.757
TER 1981 PEN 360
HETATM 1982 OPT PEN 360 14.635 12.986 35.970
TER 1983 PEN 360
HETATM 1984 OPT PEN 360 12.466 14.382 36.038
TER 1985 PEN 360
HETATM 1986 OPT PEN 360 24.369 14.310 35.501
TER 1987 PEN 360
HETATM 1988 OPT PEN 360 25.726 13.298 35.691
TER 1989 PEN 360
HETATM 1990 OPT PEN 360 26.268 9.944 35.911
TER 1991 PEN 360
HETATM 1992 OPT PEN 360 12.573 16.790 35.762
TER 1993 PEN 360
END
*PS: Any suggestion/correction for adding this whole pentosidine residue is
welcome.*
On Mon, Mar 22, 2010 at 12:16 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > Created a new atom named: CO within residue: .R<CAT 175>
> > Added missing heavy atom: .R<CAT 175>.A<C0 1>
>
> This is strange, because adding a missing heavy atom implies that
> there is a template for CAT, yet the same atom name is not being
> recognized in the pdb file.
>
> Bill
>
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Received on Fri Mar 26 2010 - 00:00:04 PDT
