AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Dec 27 2006 - 00:25:41 CST

In addition, can you show me one of your modofied
residue PDB?

Best regards.

Fenghui Fan

--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:

> 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
> following:
>
> 1. $AMBERHOME/exe/xleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99
> 2. model=loadpdb "your pdb file name"
> 3. Add water box or not.
> 4. saveamberparm.
>
> Best regards.
>
> Fenghui Fan
>
> --- Seth Lilavivat <sethl_at_gatech.edu> 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,
> > SETH
> >
> >
>
>
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