[gmx-users] define atoms

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 10 13:10:46 CEST 2009

shahrbanoo karbalaee wrote:
> Dear mark
> excuse me. I attempt it again.in analysis result of md peptide I have
> the table t  consist of atoms number column and the other  column
> rmsd(nm).I want to know what is  thename of  atom which define
> number 12 in  backbone group ?Is it NCC  for example related to  ser
> or another  aminoacid ? Do I have to by hand or software spdbv. which
> program is define number of atoms?in topology top number of atom is
> defined but it is not compatible in backbone group.
> thanks again

RMSD or RMSF?  RMSD should not be broken down by atom, I think.  In any case, 
atom 12 in the analysis should be whatever atom 12 is in the topology/structure.

If you can provide a copy-paste example of where you think the problem is 
occurring, that may help; I am still not entirely clear what the problem is.



Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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