Thanks for your help. It did work.
----- Original Message ----
From: Jianyin Shao <jyshao2004.gmail.com>
To: amber.scripps.edu
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 <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 - 06:07:22 PDT
