[gmx-users] N-terminus charge

[Erik Lindahl]

Germana Paterlini wrote:

> I am new to the list.
> The following questions may be an old one... but it is painfull to 
> search in the archive when e-mails don't have subjects...
>  
> I am using pdb2gmx with the "-ter" option to choose the charge of the 
> N- and C-termina.
>  
> My original pdb file contains a NH3+ and a COO-.
>  
> pdb2gmx correctly converts the COO- to COOH. However, the NH3+ did 
> not changed to NH2.
> As a way around, I eliminated the hydrogens of NH3+ from the PDB file 
> and then pdb2gmx gave me an NH2
> group. However, the nitrogen type is listed as "NL". Shouldn't this be 
> an "NT" ?
> Is this a bug in the TBD file (I used ffG3b1-n)?
>  

Not really; by default pdb2gmx won't remove any atoms already present, 
but you can use the -ignh option to ignore (and rebuild) all hydrogens 
in the file.

Cheers,

Erik