On Tue, Apr 07, 2009, taufik.alsarraj.utoronto.ca wrote:
> I am using top2mol2 to convert amber files *.prmtop (*.inpcrd or *.rst)
> to create mol2 files. I notice that my residue names are changing every
> time i do this.
> In the original mol2 file, the residues are Sur, Smcc, A5 DT DT etc
> after salvation with xleap and a minimization with sander i use top2mol2
> to create a new mol2 file. I found the reason why my residue names are
> changing is because in *.prmtop file only three characters are used for
> residues.
Sounds like this is the problem. The pdb format (for biomolecules) only
allows three characters for atom names, and LEaP conversion probably
maintains this restriction. (Generally, PDB-format files, rather than
mol2 format files, are used for input to LEaP). I'm not sure that it
is easy to have residue names in Amber more than three characters long,
although there is no fundamental reason for this -- just that we would
have figure out what to do when asked to write PDB files if the names are
longer than that allowed.
You could try building the prmtop file with sleap, to see what
happens....but you should also consider if there is any way to use
three-letter residue names exclusively.
....good luck....dac
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Received on Wed Apr 08 2009 - 01:19:55 PDT
