[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature
feenstra at few.vu.nl
Tue Jun 21 17:45:33 CEST 2005
Sandeep Somani wrote:
> As you mentioned I had listed the entries i made to all the
> parameter files ( ffoplsaa.atp ffoplsaa.rtp ffoplsaanb.itp ffoplsaa.hdb
> ffoplsaabon.itp ) in my mail. i know the mail was too long!
> basically my question was --
> is there is any convention to be followed for naming hydrogens
> in any new molecule ?
The short answer is: No.
However, pdb2gmx does follow strict rules for naming hydrogens it adds
according to the hydrogen database (.hdb), see manual for details.
In addition, for several classes of molecules (e.g., proteins, nucleic
acids), there are naming conventions.
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