Developing topologies for modified NA residues?

From: Jacob Pøhlsgaard (
Date: Mon Apr 10 2006 - 08:37:04 CDT

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?
 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?
 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 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

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