[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature
feenstra at few.vu.nl
Thu Jun 23 10:01:40 CEST 2005
Sandeep Somani wrote:
> Hi Anton
> The reason I asked the question was that the atom type (HG) added to the
> output .top and .gro file
> was not in any of the input parameter files. I made sure to delete
> everything except my entries.
> so i was wondering if there are any hardcoded atom types in pdb2gmx
> which are not picked from the parameter files.
No. But there are in addition to the files you provide, also the library
files. You'll want to check the ff*.hdb file (for your forcefield).
In the output of pdb2gmx you will find a line like:
Opening library file: /usr/local/share/gromacs/top/ffG43a1.hdb
* NOTE: New Phone & Fax numbers (below) *
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