[gmx-users] Adding Hydrogens by pdb2gmx

James Starlight jmsstarlight at gmail.com
Mon Oct 31 14:09:03 CET 2011


all hydrogens were represented as a part of the groupd in wich they were.
So is there possible way to explicit it?

Another question about pdb2gmx. about -term
as I understood this must be used only if atoms for CAP groups are
presented in the PDB file mustnt it?
So what term exactly do? Doest it make a connection beetween CAP and C and
N termi or anothing else?


2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
>>  with gromos force field
>> I've checked conf.gro by VMD and this structure didnt contains any
>> hydrogens ;o
> I highly doubt that.  I've used one of the Gromos96 force fields for
> nearly all of my work and it has never failed in any Gromacs version.
>  Perhaps you're simply not taking into account the fact that Gromos96
> parameter sets are united atom, meaning that aliphatic hydrogens are not
> represented explicitly.
> -Justin
> --
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