[gmx-users] pdb atom nomenclature in gmx rtp files

Alan alanwilter at gmail.com
Tue Aug 10 16:26:03 CEST 2010

Hi there,

I see in ffoplsaa.rtp that, e.g., CYS has:

   HB1    opls_140    0.060     2
   HB2    opls_140    0.060     2

But according to latest PDB atom nomenclature it should be:

HB2 ...
HB3 ...

Of course that using pdb2gmx -ignh and it should avoid this problem,
but unless for any other specific reason, I find this quite annoying.

GMX 4.5 still doesn't address this.

So, is there plans to bring rtp atom nomenclature to the latest PDB
standards or this task is not necessary (and I missing something else)
or only in gmx 5 when pdb2gmx gets smarter?

Many thanks in advance,

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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