Re: Developing topologies for modified NA residues?

From: Jan Saam (
Date: Mon Apr 10 2006 - 11:23:39 CDT

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.


> 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
+49 30 450-528-446

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