Hello Mani.
>From your PDB I can see that you have several mis-named or duplicated atoms
like 51 H' ' and 55 H2' '. Those atom types wont be recognized by the force
field. Also, why no use AmberTools nucgen to build your DNA molecule? See
tutorial 1 in the amber homepage.
Hope this helps.
Have a good day!
Rodrigo.
2011/8/8 manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
> Hi All,
> I am trying to prepare prmtop and inpcrd files for uncomplex DNA-22mer
> using
> xleap of amber10. I have downloaded the pdb file from the protein data
> bank
> and made required modification. Still xleap is unable to save the files, as
> it is complaining about the atom type. Attached is the modified pdb
> file. I never handled DNA stuff with amber any suggestions.
>
>
> mani
>
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Received on Mon Aug 08 2011 - 14:00:04 PDT
