VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Jan 17 2017 - 07:17:02 CST

Hi,

You probably need to specify the segment with the psfSegID option. Check
the correct value with a VMD command like:
[atomselect 0 "<selection text>"] get segname

Jerome

On 16 January 2017 at 01:36, Bin Sun <sunbinhrx_at_gmail.com> wrote:

> Hi All,
> I want to use the cv module of VMD to calculate the alpha-helical content
> of a peptide(24 residues). I first loaded the pdb file and then open the Tk
> console. The following content was typed into the console:
> =====================
> cv molid 0
> cv config {
> colvar {
> name alpha_content
> alpha {
> residueRange 1-24
> }
> }
> }
> =======================
> However, the above command does not give the right result, instead, en
> error message appeared saying "Error: could not find atom "O" in residue
> XX(1-24), segment "MAIN" ". I doubled checked the pdb file and be sure that
> no atom is missing.
>
> Could anybody give some advice about this error ?
>
> Thanks in advance !
>
> Best,
> Bin
>