Hello,
This does not really answer your entire question, but is worth
pointing out. Do not add to or subtract from the parm files included
with the source, especially if there's a chance that copy will pass on
to others. Another reason you should avoid this is because if you
upgrade your ambertools package, any changes you make could
conceivably be overwritten.
Thus, put any new/updated parameters and/or atom types into an frcmod
file that you load into leap.
On Thu, Mar 25, 2010 at 11:34 PM, sikander azam <syedazam2008.gmail.com> wrote:
> 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
This section of the PDB file looks very strange to me. Is OPT your
atom name? Why are all atom names the same? Why do you have so many
ter cards? What this looks like to me is a collection of a very large
number of single-atom residues (like counterions). Perhaps I am
wrong, but that's how I'm reading it. It's hard to see how this is
related to pentosidine... I am too confused here to offer any further
help (if what i offered before can actually be considered help).
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Mar 26 2010 - 00:00:05 PDT
