AMBER Archive (2008)
Subject: Re: AMBER: mask for oligosaccharide
From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Thanks for your help. It did work.
On Wed, Jul 30, 2008 at 12:23 PM, Wenyong Tong <wenyong_tong_at_yahoo.com> wrote:
Here is my measure_rmsd.trajin:
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.