VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Aug 03 2007 - 02:59:02 CDT

Dear Shulin,

This is actually more a VMD issue, so in the future please post VMD
issues to the VMD list ;).

> I just do a MD simulations of a small protein using NAMD soft, now, I want
> to calculate the C alpha RMSD of the protein from the trajectory. Using VMD,
> only the backbone RMSD can be calculated.

In the RMSD trajectory tool, you should select "trace" instead of
"backbone". In that way, you'll compute the RMSD only for the Calpha
trace.

> Another question:
> For hydrogen analysis, how to calculate the hydrogen bond like soft PTRAJ.
> PTRAJ can easily calculate many kind of RMSD from Amber or charmm
> trajectory. How can we use ptraj to analyze trajectory produced by NAMD.

As far as I know, PTRAJ can read dcd trajectory files. You can also
compute h-bonds with VMD (you need a script for that purpose), so
consider it as an option.

Cheers,
Michel