AMBER Archive (2008)


From: David A. Case (
Date: Thu Jan 10 2008 - 21:32:30 CST

On Thu, Jan 10, 2008, Shozeb Haider wrote:
> I am trying to simulate a modified pentapeptide. On running antechamber
> the -rn flag labels the entire pentapeptide as single unit (MOL
> default). When I then load it in xleap and set up the system it is only
> recognised as one long molecule. In other words, the peptides do not
> retain their name labels. Is there some way one can prevent antechamber
> from adding in the name label ? or allow it to use the original labels.

Antechamber is not designed to handle multiple residues; rather, it is
designed for small-ish molecules or single residues. You can probably have
antechamber create a mol2 file, then hand-edit it to split it back into 5
separate peptides.


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