On Wed, Jul 30, 2008 at 12:23 PM, Wenyong Tong <wenyong_tong.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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Received on Sun Aug 03 2008 - 06:07:18 PDT
