[AMBER] Average structure vs Individual frames

From: Yin, Guowei <guowei_yin.med.unc.edu>
Date: Tue, 14 May 2019 01:16:59 +0000

Hello all,

My protein contains GDP and Mg2+. After the simulation, I look up the individual frames and the average structure over the 50 ns. I found in the individual frames the Mg2+ stays close to the phosophates of GDP and leads to the artificial bonds recognized by the PyMol. But in the average structure, the distance looks fine and no artificial bonds by PyMol. I attached the screenshot below. This is something with the processing?

The parameters used for Mg is:
Oelschlaeger et al JMB 2007 Mg dummy and MD6.

When I generate the final trajectory, I used the unwrap as:

unwrap :1-169

center :1-169 mass origin

image origin center familiar

and the way I generate the average structure is:

cpptraj ../proteinA.top <<eof

trajin ./proteinA.mdcrd 25000 50000 1

rms first

average proteinA.avg.pdb pdb


The average structure

individual frames:


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Received on Mon May 13 2019 - 18:30:02 PDT
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