On Mon, Nov 22, 2004, Cenk Andac wrote:
> I am having some difficulty converting amber prep format to mol2 format.
>
> My molecule (TAR) is a 16nt-RNA hairpin with the following sequence which is
> in accordance with the all_nucleic94.lib.
> 5'- RG5 RA RG RC RC RC RU RG RG RG RA RG RG RC RU RC3 - 3'
Neither the prep nor the mol2 formats, as implemented in Amber, are well
designed for multiresidue macromolecules; they were both intended to be used
for single residues.
If you have amber prep files for the residues, you could use leap to create a
pdb file for the full length sequence. Then ambpdb with the "-pqr" option
would get you a file with partial charges, but not in mol2 format. At that
point, you would probably be faced with writing your own script to complete the
task. I think there is no good way at present to get antechamber or Amber to
write a macromolecular mol2 format file.
....dac
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Received on Tue Nov 23 2004 - 16:53:00 PST
