[gmx-users] non-standard atom names

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 20 19:22:10 CEST 2009

Stefano Meliga wrote:
> Hello,
> I noticed that the command editconf -i structure.gro -o structure.pdb 
> produce a pdb file in which some atom names are not standard.
> In particular the delta carbon on ILE:
> "CD  ILE" should be "CD1 ILE";
> and the oxigens of the C-terminus
> "O1" should be "O "
> "O2" should be "OXT".
> This is particularly annoying when GROMACS' output pdb is then used in 
> input of other software, e.g. FIRST.
> You might want to fix this.

I think "should be" is a matter of perspective.  The atoms are named according 
to GROMACS convention, and are used consistently within all force field files 
(.rtp, .tdb, etc).  If you are aware of inconsistencies with other programs, I 
would think a few simple find-and-replace commands in a text editor (or 
scripting, awk, sed, etc) would solve the problem, without a re-write of 
numerous GROMACS files (and code?).


> Sincerely,
> Stefano
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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