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.
....dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 13 2008 - 06:07:19 PST
