Hi Yunierkis,
This is normal - There is an explanation as to why and an example of some
more meaniful analysis (such as cluster analysis) here:
http://ambermd.org/tutorials/basic/tutorial3/
Good luck,
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Yunierkis Perez Castillo
> Sent: Saturday, October 04, 2008 6:26 AM
> To: amber.scripps.edu
> Subject: AMBER: ptraj average structure
>
> Hi all.
> I have been trying to use ptraj in order to obtain an average structure of
> a 10 ns MD simulation of a protein. Here is my ptraj input file:
>
> trajin ../protein.crd
> center :1-634
> image center familiar
> rms first mass out 10ns_CA_rms.csv :1-635.CA
> average 10ns_aver_box.pdb :1-635 pdb
>
> After looking at the average structure I can see that some residues have
> very unrealistic geometries (overlapping atoms). By searching the amberY
> mailing list I found that this is a common problem of calculating average
> structures with ptraj, mainly due to high flexibility residues. Is there
> any way a could obtain average structures from amber trajectories lacking
> this problems?
> Thanks in advance for any help
> yunierkis
>
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Received on Sun Oct 05 2008 - 05:10:35 PDT
