[gmx-users] how to add a PTR residue into the gromacs simulations

Marc F. Lensink lensink at scmbb.ulb.ac.be
Sun Mar 11 09:17:36 CET 2007

On Sun, Mar 11, 2007 at 05:16:04PM +1100, Mark Abraham wrote:
> Marc F. Lensink wrote:
> >hi tom,
> >
> >>the pdb2gmx is unable to convert a peptide bound to a protein because it 
> >>does not recognise the PTR (phosphotyrosine) in the peptide.  Gromacs 
> >>manual says that you can only resolved this
> >>by changing the adding the residue to the rtp files.  The problem now is 
> >>that I do not have writing privileges for these files on our University  
> >>cluster.  Is there any other (easy) way to resolve this?
> >
> >copy the files you want to edit into your working directory.
> I suspect that in order to have pdb2gmx find the modified files, Tom 
> needs to make a full copy of the gromacs/share/top directory in his own 
> filespace, set the environment variable GMXLIB to that path, and then to 
> edit as necessary.

true, unless it's '.'.


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