AMBER: bad connectivity - more detail

From: Seth Lilavivat <>
Date: Tue, 26 Dec 2006 13:02:27 -0500

Dear Amber Community,

I am a novice AMBER user, creating modified nucleic acid structures. The
current model that I am working on is a bicyclo RNA structure. Here is a brief
summary of my current protocol:

1. Start with closest residue, in this case RA5, RA, RA3, RU5, RU, and RU3
2. Modifiy them in xleap to have the correct structure.
3. Create a residue library file in one of the following two ways:
   1. Generate a PDB of the new residue, then use antechamber to parameterize
   2. Save the modified residue as a prep file from xleap. Then switch out all
of the partial charges by hand, check all of the atom types, and try and modify
necessary force field parameters.

One problem that I am running into is:

Connectivity - when use antechamber/gaff generated prep residues, I get a link
from C4 (if it is an A) to O1P or O2 to O1P (if it is a U). The link should be
from the O2* to the P (since this is a 5' - 2' structure).

Attached are some residue files and a pdb. I hope this helps.


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Received on Wed Dec 27 2006 - 06:07:54 PST
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