Re: Reverse Coarse Graining using VMD CG Builder

From: Peter Freddolino (
Date: Wed Oct 21 2015 - 10:49:38 CDT

Can you post the rcg file and CG_Lipid.pdb file? It sounds like this should work fine.

> On Oct 21, 2015, at 11:41 AM, Ardavan Mehdizadeh <> wrote:
> Dear Peter,
> Many thanks for replying,
> Yes, I did. I split the structure into two separate part, one CG_Lipid.pdb another CG_Peptide.pdb also I did the same for All-Atom structure (AA_Lipid.pdb & AA_Peptide.pdb). That's why I've said there is no problem with Pepdite Reverse Coarse Graining and I get the mentioned error for Lipid bi-layer Reverse Coarse Graining.
> I want to mention it again that I've created CG structure in a same way which I want to create AA structure. First I've create AA structures of Peptide and Lipid bi-layer the I've created CG structure of Peptide and Lipid bi-layer separately (where I got two RCG files) then I merged CG structures of Peptide and Lipide bi-layer and finally solved them in a water box and ran SMD simulation.
> Thanks,
> Ardavan.
> On Wed, Oct 21, 2015 at 3:59 PM, Peter Freddolino <> wrote:
> Hi Ardavan,
> The problem is almost assuredly the fact that your rcg file numbering does not match what is actually present. If you assembled a combined all-atom system with the atoms in the same order as they are in your merged file, and then coarse grained that, you could use the resulting rcg file. Alternatively, did you try splitting the structure into separate lipid and peptide pdb files for reverse coarse graining?
> Best,
> Peter
> > On Oct 21, 2015, at 4:15 AM, Ardavan Mehdizadeh <> wrote:
> >
> > Dear NAMD users, Hi
> > I have a coarse grained SMD simulation result which contain a Peptide, Lipid bi-layer solved in a water box. At first, I used VMD CG Builder to create RBCG Molde of Lipid bi-layer and a Peptide separately then I merged them () and solved in a water box; Meaning I have 2 RCG file (one for Peptide another for Lipid bi-layer).
> > After a SMD run, I tried to change one frame of DCD file (which saved as a pdb file) to All Atom again using Reverse Residue-Based CG (VMD).
> > There is no problem for Peptide, but I get an error for Lipid bi-layer which is written below. I really need someone to help me with that and I deeply appreciate your help.
> >
> > Thanks,
> > Ardavan.
> >
> > Error: vescsub: two vectors don't have the same size
> > vecsub: two vectors don't have the same size
> > while executing
> > "vecsub $cgcen $aacen"
> > (procedure "::cgtools::apply_reversal" line 38)
> > invoked from within
> > "::cgtools::apply_reversal $::cggui::currentFromCGMol $::cggui::revcgfile $::cggui::currentFromCGAAMol $::cggui::fromCGoutpdbfile $::cggui::do_rot.."
> > (procedure "::cggui::buildAAModelExecute" line 29)
> > invoked from within
> > "::cggui::buildAAModelExecute"
> > invoked from within
> > ".cggui.fromCGFrame.applyDB invoke"
> > ("uplevel" body line 1)
> > invoked from within
> > "uplevel #0 [list $w invoke]"
> > (procedure "tk::ButtonUp" line 24)
> > invoked from within
> > "tk::ButtonUp .cggui.fromCGFrame.applyDB"
> > (command bound to event)
> >

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