AMBER Archive (2009)

Subject: Re: [AMBER] mol2 file to amber pdb file format

From: David A. Case (
Date: Thu Jun 04 2009 - 11:55:39 CDT

On Thu, Jun 04, 2009, balaji nagarajan wrote:
> I have a doubt regarding how to generate amber atom types for the molecules
> from mol2 files generated from smiles string ?
> the molecules are nucleotides

Look at $AMBERHOME/dat/leap/prep/, which has the Amber atom
types for each atom name. Then edit the mol2 to put in the correct atom
types. (This only works if you are using standard nucleotides.)

You could also try antechamber with the "-at amber" flag.


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