AMBER Archive (2008)

Subject: Re: AMBER: mask for oligosaccharide

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Jul 30 2008 - 17:26:31 CDT

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

>
>
> Ask again, sorry.
>
> Here is my measure_rmsd.trajin:
>
> trajin equil_2.crd
> trajin equil_3.crd
> trajin gc.md.x
> 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.

Best,

Jianyin Shao

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