VMD-L Mailing List

From: Emiliano Fratini (fratini_at_csgi.unifi.it)
Date: Thu Mar 09 2017 - 05:34:41 CST

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