[AMBER] Enquiring about RMSD of small and large proteins

From: Yip Yew Mun <yipy0005.gmail.com>
Date: Mon, 8 Sep 2014 10:52:54 +0800

Hi, I recently ran a simulation of a small alpha helix (~12 residues) with REMD and I did a RMSD analysis using just the backbone atoms (N,CA,C). Usually for simulations of large proteins, an RMSD of 3 Angstroms is usually enough to quantify that there are no major conformational changes. However, I realised for small protein systems like mine, an RMSD of 3 Angstroms isnít a good criterion to say that I have folded my protein successfully. Therefore, I wish to ask:

1) Does the number of atoms affect the RMSD calculation?
2) Is there a need for the reference structure to be protonated before using it for RMSD analysis since in this case, Iím just using the backbone atoms (N,CA,C).

Thanks.

Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry & Biological Chemistry
School of Physical & Mathematical Sciences | Nanyang Technological University | Singapore 639798
Tel: (+65) 97967803 | Email: yipy0010.e.ntu.edu.sg | GMT+8h

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Received on Sun Sep 07 2014 - 20:00:04 PDT
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