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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 11 07:16:04 CET 2007

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.


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