Re: AMBER: mask for oligosaccharide

From: Jianyin Shao <>
Date: Wed, 30 Jul 2008 16:26:31 -0600

On Wed, Jul 30, 2008 at 12:23 PM, Wenyong Tong <>wrote:

> Ask again, sorry.
> Here is my measure_rmsd.trajin:
> trajin equil_2.crd
> trajin equil_3.crd
> trajin
> reference gc_annMD_min_2.rst (from NMR refinement)
> strip :WAT :Na+

I think this command does not work properly. There should be no space
between :WAT and :Na+. So the sodium ions are not removed from the system,
which will be included in your next rms calculation. Use "strip :WAT,:Na+"
instead please.

> rms reference out rmsd_to_NMR.dat
> My question is how to define the mask for sugar (e.g. rms reference out
> rmsd_to_NMR.dat .C, O, H ???). If I did not define, the result is different
> from the one calculated from VMD.

If you want all atoms in the whole residue, you can just use :RES.


Jianyin Shao

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Sun Aug 03 2008 - 06:07:18 PDT
Custom Search