Building a pdb file

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Tue Jul 03 2007 - 16:14:41 CDT

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:
http://chemistry.gsu.edu/glactone/PDB/DNA_RNA/dna.html

2) At the suggestion of the archives of the namd-l listserv,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5086.html and
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5087.html , 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X-View is outdated as well.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 (
http://hugin.ethz.ch/wuthrich/software/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is no longer maintained.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,
http://hugin.ethz.ch/wuthrich/software/molmol/man/config.htm , 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

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