AMBER Archive (2008)

Subject: Re: AMBER: mask for oligosaccharide

From: Wenyong Tong (
Date: Wed Jul 30 2008 - 23:13:08 CDT

Thanks for your help. It did work.

----- Original Message ----
From: Jianyin Shao <>
Sent: Wednesday, July 30, 2008 6:26:31 PM
Subject: Re: AMBER: mask for oligosaccharide

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
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

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