VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Sep 24 2018 - 21:59:09 CDT

Dear Kimberly,
Just a couple of thoughts on this, which I'm posting partly because there
have been a couple of questions about the VMD RBCG model lately.

First, I'd like to point out that the RBCG model included in VMD is quite
old at this point; one really ought to be using a recent martini version
instead. As NAMD supports the martini FF now, all that would really be
required would be to use appropriate cgc files and corresponding toppar
files (see examples with the tutorial at
https://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf) - one
ought to double check that those are appropriate for the up-to-date version
of the martini FF that you want to use. I raise this point only because the
default RBCG conversion files used by vmd corresponds to a CG
representation that really shouldn't be used for starting new projects any
more since it is superseded by recent martini versions.

Second, using recent martini versions will instantly fix your calcium
problem (sort of), in that martini includes a topology for a (implicitly
hydrated) calcium ion. Read the comments in the martini topology carefully
for caveats.

Third, you may want to think carefully, for your system, about whether it
is better to treat your calcium ion as a calcium ion, or come up with some
way of implicitly incorporating it into your protein topology. That might
be a better option if it is a site bound calcium and you're not interested
in letting it dissociate (especially as the martini free calcium is really
supposed to represent calcium with a solvation shell).

Best,
Peter

On Mon, Sep 24, 2018 at 2:27 PM, Lewis, Kimberly A <
lewiskim13_at_students.ecu.edu> wrote:

> Hello,
>
> When using VMD, specifically the residue based course grain builder, I
> know there is the protein and water sets that you can add to use. Is there
> something that will create Ions as a bead, that are bound to the protein
> such as Calcium? When I have tried so far, the beads are generated for the
> amino acids but the calcium ions are missing from the cg pdb.
>
>
> Thank You,
>
> Kimberly Lewis
>
>
> East Carolina University
>
> Department of Chemistry
>