VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Mar 09 2017 - 07:06:56 CST

Hi Emiliano,
Could you please provide a little more information on a couple of points?
-what version of vmd are you using?
-what topology files is autopsf trying to use?

Thanks,
Peter

> On Mar 9, 2017, at 6:34 AM, Emiliano Fratini <fratini_at_csgi.unifi.it> wrote:
>
> Hi all,
> I’m trying to coarse grain half an antibody (1igy.pdb). I selected only one short chain and the corresponding long chain,
> all the rest is discarded while generating the all atoms PSF file.
>
> Since I’m not an expert in CG I’m following the tutorial
> “Residue-based coarse graining using MARTINI Force Field in NAMD”.
>
> Everything goes ok till I try to generate the PSF file from the CG PDB file obtained
> from the CGbuilder (residue based).
>
> AutoPSF stops with an error when trying to "guess and split chains using current selections”
> The Error is: can’t read “Ccoords”: no such variable
>
> I’m a bit lost, anyone has any idea?
>
> thanks a lot,
> e
>