VMD-L Mailing List

From: Audrey Salazar (alsalazar_at_northwestern.edu)
Date: Mon Aug 06 2007 - 11:16:12 CDT

Dear VMD-L,
I am a first year graduate student studying nucleic acids using the
all27 force field in NAMD. At present, I am interested in making a
short, single stranded RNA solvated with water molecules in VMD.
Below, I outline my procedure intermingled with questions, highlighted
by the **. I would appreciate any help that the VMD community might
be able to provide.

I created a pdb file that contains the coordinates for atoms in a 3
base long single stranded RNA (sequence= GCA). I then solvated the RNA
and generated a psf and pdb file (for the RNA-water system) using
Extensions--> Modelling --> Automatic PSF Builder. In this window, I
performed the following operations:

Step 1) I added the topology (top_all27_na.rtf) and parameter
(par_all27_na.prm) files that I obtained from
http://www.pharmacy.umaryland.edu/faculty/amackere/research.html. I
clicked "load". (No problems here)

Step 2) I included "Everything" and clicked "Guess and split chains
using current selections." Three lines of text appeared in the "Chains
Identified" box:
N1 3 1- 62 5TER 3TER RNA
N2 3 63- 66 5TER 3TER RNA
N3 1 67- 67 5TER 3TER DNA
and of the three lines, I kept the ones that had "RNA" in the "Type" column.

** I am unclear as to the meaning of the output above. Does each row
correspond to one chain? Is there any documentation as to what the
columns headings stand for in the "Chains Identified" box?

** Should I have deleted one of the RNA lines too? I.e. should I only
see one line of text if there is only a single molecule in the pdb
file?

Step 3) I selected "solvate" under Extras at the bottom of the screen
and I clicked create chains.

Next, I checked the psf and pdb generated by VMD in VMD and I get what
appears to be one chain surrounded by a water box. My pdb looks
correct, but with more than 8000 atoms, reading through it line by
line is a daunting task and I am not sure if I have two chains that
are superimposed on each other (because of what I did in step 2).

Thank you in advance.

Audrey Salazar 

-- 
Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA