From: FyD <>
Date: Fri, 11 Jan 2008 08:53:04 +0100

Quoting Shozeb Haider <>:
> 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.

Usually when you derive charges you do it for a _small_ molecule. This
small molecule is usually a single residue to build a force field
library for this small molecule (or a fragment built from this small

That being said, you can use R.E.D. where the final output is the
Tripos mol2 file format, and where multiple residue naming is fully handled.

See for instance the "W-59" R.E.DD.B. project with the corresponding
Tripos mol2 file available:

regards, Francois

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Received on Sun Jan 13 2008 - 06:07:21 PST
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