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.
Mark
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