AMBER Archive (2005)

Subject: AMBER: average structure-ptraj

From: xueping (xueping22_at_yahoo.com)
Date: Sat Apr 09 2005 - 03:23:23 CDT

Dear all,

I am having problem again to generate my average
structure using ptraj, this is my script:

trajin ../PfCo.md1.mdcrd
trajin ../PfCo.md2.mdcrd
trajin ../PfCo.md3.mdcrd
trajin ../PfCo.md4.mdcrd
trajin ../PfCo.md5.mdcrd
average PfCo_average.pdb pdb nowrap

i viewed my PfCo_average.pdb file in vmd, the
structure
is not correct, in the vmd console, it stated that
unusual bonding within certain residue to certain
residue...

then i try to convert my last rst file to pdb file n
view it, it is ok...meaning my simulation shouldn't
have any problem rite?

I try to generate average structure using single mdcrd
file, it gives me the same error too... Please give me
some suggestions.

Thank you very much..

Regards
xueping

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