AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: Fenghui Fan (
Date: Tue Dec 26 2006 - 22:19:41 CST

I do not know the reason why you want get the prep
file. It seems not necessary for your purpose.

As you already have your pdb file,just do as the

1. $AMBERHOME/exe/xleap -s -f
2. model=loadpdb "your pdb file name"
3. Add water box or not.
4. saveamberparm.

Best regards.

Fenghui Fan

--- Seth Lilavivat <> wrote:

> 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.
> Thanks,

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