Re: Reverse Coarse Graining using VMD CG Builder

From: Ardavan Mehdizadeh (
Date: Wed Oct 21 2015 - 10:41:55 CDT

   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.


On Wed, Oct 21, 2015 at 3:59 PM, Peter Freddolino <>

> 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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