AMBER Archive (2006)

Subject: AMBER: How to create a modified NA in leap

From: sethl_at_gatech.edu
Date: Fri Aug 25 2006 - 15:20:35 CDT

Dear Amber Community,

I am wanting to create a modified nucleic acid residue in xleap. I want to
create a nucleic acid with a modified sugar (a hexose). So far I just edited
one of the standard residues and "saveamberprep". When I try to use this
residue I get the following errors

"Loading Prep file: /home/seth/amberfiles/NewResidues/hexA5.in
residue leap-generated prep residue atom C31: chain type [1.510962] must be 1
character
Loading Prep file: /home/seth/amberfiles/NewResidues/hexA.in
residue leap-generated prep residue atom C33: chain type [3.674663] must be 1
character
Loading Prep file: /home/seth/amberfiles/NewResidues/hexA3.in
residue leap-generated prep residue atom C34: chain type [4.035477] must be 1
character
Loading Prep file: /home/seth/amberfiles/NewResidues/hexT5.in
residue leap-generated prep residue atom C31: chain type [2.323271] must be 1
character
Loading Prep file: /home/seth/amberfiles/NewResidues/hexT.in
residue leap-generated prep residue atom C33: chain type [4.027224] must be 1
character
Loading Prep file: /home/seth/amberfiles/NewResidues/hexT3.in
residue leap-generated prep residue atom C34: chain type [4.061176] must be 1
character"

What am I doing wrong?

Thanks,
SETH

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