AMBER Archive (2004)

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

From: david.evans_at_ulsop.ac.uk
Date: Tue Nov 23 2004 - 11:06:22 CST

>> 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

Babel claims to convert from prep to mol2, and from pdb to mol2,
though the latter doesn't deal with charges in the pdb file. I've
never tried prep to mol2 myself...

Dave
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu