Re: Building a pdb file

From: Peter Freddolino (
Date: Tue Jul 03 2007 - 16:43:14 CDT

Hi Audrey,
for now, for building RNA you may want to have a look at nucgen
distributed with AMBER). I have not used it myself, but as far as I know
it should do what you want. I'm hoping to make the molefacture plugin of
VMD usable for all of this kind of structure building, but I haven't yet
had time to finish the nucleic acid builder.

Audrey Salazar wrote:
> Dear NAMD list,
> I am a first year graduate student and I hope to model small RNA in
> NAMD. As a test case, I hope to build a pdb for a single stranded RNA
> with 2 nucleotides (for e.g. GG). Thus far, I am having troubles
> locating or creating this file. Does anyone have any suggestions? I
> will delineate what I have already tried below:
> 1) I located pdb files for single nucleotides under the RNA
> nucleotides section on the following webpage:
> <>
> 2) At the suggestion of the archives of the namd-l listserv,
> <>
> and
> , I located namot. The program has fallen into disuse and does not
> appear to be compatible with a version of Motif supported by our
> version of RHE and X-View is outdated as well. I decided to search
> for a different program.
> 3) I located a program called MOLMOL
> ( that is capable of
> reading and writing pdb files. I have been able to successfully
> compile the program, but very little information is available on it
> and the mailing list is no longer maintained. Using the default
> library ( Amber94.lib), I have been unable to see then entire
> structure of the G rna nucleotide that I downloaded from the website
> in section 1. When I import the pdb into MOLMOL, the program
> complains that there are residues contained in the pdb that are not
> defined in the default pdb library, and thus part of the nucleotide is
> not visible in the MOLMOL viewer. I followed the suggestions listed
> under "Residue Libraries" here,
> , to no
> avail.
> Any recommendations on how to build a pdb from scratch or from smaller
> chunks of pdbs would be greatly appreciated.
> Thank you in advance,
> Audrey
> --
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering Phone: 847.491.2188
> Northwestern University
> Evanston, IL USA

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:55 CST