From: Peter Freddolino (
Date: Mon Aug 06 2007 - 11:46:46 CDT

Hi Audrey,
a couple of notes; hopefully this is helpful:

Audrey Salazar wrote:
> Step 1) I added the topology (top_all27_na.rtf) and parameter
> (par_all27_na.prm) files that I obtained from
> I
> clicked "load". (No problems here)
Parameter files shouldn't be included here; only topology files
> 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?
Each row corresponds to one chain. It seems odd in your case that
multiple separate chains were identified; you should have a look at the
second and third chain and see what they actually consist of (clicking
on them in the chains identified box will highlight them in the main vmd
opengl window). I will try to clarify the docs on the column headings;
for the record, the ones which might be ambiguous are Length (number of
residues), Index Range (serial numbers of the atoms in the chain), and
Nter/Cter (which will be relabeled First/Last in the next release to be
less protein-centric, and correspond to the patches applied to the first
and last residues in the chain
> ** 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?
Probably. You may need to instead merge them by editing the first chain
to include all of the atoms, if for some reason a chain break is being
introduced where there shouldn't be one. You can do this by deleting the
second and third chain, and then clicking "Edit Chain" with the first
one highlighted, typing the selection all into the selection box,
clicking get indices, and then applying these changes.
> 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).
Probably best to just look at the RNA lines, which should be a fairly
modest component.

> Thank you in advance.
> Audrey Salazar