AMBER Archive (2004)

Subject: Re: AMBER: Problem with converting AMBER PREP to MOL2

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 23 2004 - 10:12:06 CST


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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