Re: Developing topologies for modified NA residues?

From: L. Michel Espinoza-Fonseca (
Date: Mon Apr 10 2006 - 12:00:55 CDT

That's right! what happened with paratool, I'm anxiously waiting for
the user's guide :-D

2006/4/10, Jan Saam <>:
> Hi Jacob,
> Jacob Pøhlsgaard wrote:
> Hi guys
> I want to run simulations of modified nucleic acid structures. Most of
> these modifications are really minor, in the form of methylations and such.
> I'm looking for a streamlined way to both develop the topology files and to
> incorporate the modifications into my structures.
> So far I've come up with the idea of simply renaming the residues in the
> PDB file, and then running psfgen on it, using a modified topology file
> containing the topologies for the methylated residues. If my topology file
> is corretly made, this should allow psfgen to add the missing methyl groups
> if I understand it correctly? You are right.
> But how do I best create the topology files? I can easily build the
> structures in a number of 3D programs, but I'm unsure of how I should
> generate the IC information from the resulting pdb (or other) formatted
> files.
> Am I correct in assuming that the IC information is what should allow
> psfgen to guess the correct coordinates for the missing atoms? Correct, but
> if the IC table is missing, psfgen has it's own logic to guess the
> positions. Of course these might be different from what you would expect.
> How do people usually do this? Is there some magic piece of softaware which
> will import a .pdb, parse it, calculate angles and bonds and write a CHARMM
> topology file from it? I thing most people tune their topology files per
> hand, others use the CHARMM program package. Unfortunately CHARMM costs
> money and not every group has a license. This is why I wrote PARATOOL, a
> plugin for vmd-1.8.4, which you can use to develop force field parameters
> for arbitrary molecules. It will result in topology and parameter files in
> CHARMM format.
> Documentation is still somewhat crappy but I'm working on it.
> So wait a couple of days until VMD-1.8.4 is out or fetch yourself one of
> the beta releases.
> Best,
> Jan
> I know I may also need parameter files, but I know some people locally who
> can help with that :)
> Best regards
> Jacob Pøhlsgaard
> Department of Biochemistry and Molecular Biology
> Denmark
> --
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
> Germany
> +49 30 450-528-446

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