VMD-L Mailing List

From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Mon Sep 24 2018 - 14:37:34 CDT

Hello Kimberly,

The RBCG builder uses mapping files to perform coarse-graining, i.e. the
transformation from atomistic to CG resolution.  These are the cgc files
you load.  If you want to transform your calcium, simply write and load
a custom cgc file.

Having said that, I would advise caution in the case of ions that you're
describing.  In the CG force field used (RBCG/Martini), each CG solvent
particle (water, ion, etc) actually corresponds to four all-atom solvent
molecules. In other words, 1 CG water = 4 AA waters, 1 CG calcium ion =
4 AA calcium ions.

This may cause you some problems, perhaps not so much with
electrostatics (since those are implictly modeled anyway), but most
likely with van der Waals interactions.

In your case, it would perhaps be better if you defined a particle for
your ion anew instead of using the predefined Qd particle, so that they
correspond to 1 ion instead of 4.

Good luck,

Fotis Baltoumas

On 09/24/2018 09:27 PM, Lewis, Kimberly A 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
> 

-- 
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Fotis A. Baltoumas
Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology, National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --------------------------------------
email : fbaltoumas_at_biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
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