AMBER Archive (2006)

Subject: Re: AMBER: bad connectivity - more detail

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Wed Dec 27 2006 - 10:26:14 CST

I need the prep files because the pdb file is one of a standard RNA duplex, not
one with the modified nucleotides. From my understanding, even if you have a
starting pdb, leap still needs to have those residues in the residue library.
Otherwise, how would leap know about partial charges and bond parameters?

The PDB that I provided is a standard RNA duplex but I removed all of the atoms
that were associated with the sugars since the structure that I am trying to
model has a modified sugar. I am essentially using the protocol found from this
mailing list archive: http://amber.ch.ic.ac.uk/archive/200610/0362.html but
without the RESP method for the charges.

Thanks
SETH

Quoting Fenghui Fan <fenghui_fan_at_yahoo.com>:

> 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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