[gmx-users] About peptide mutation with non-standard residue

[Vicente Domínguez]

Dear GROMACS users,

I am working with specific peptide formed by a repetition of pentapeptides
which sequence is VPGKG. I have built the structure of a protein formed
with a determined repetition of those pentapeptides, the function
prediction of that protein was carried out with I-TASSER server. Now, I
need to mutate a specific residue (K) in some pentapeptides for a
non-standard residue (XXXX). I have built successfully the topology of this
residue. I am trying to change a K residue for this XXXX residue using
several ways and several tools, for example, UCSF Chimera with Join Models
tools. The problem always is that I reach a .pdb file with the final
structure but I can not use a pdb2gmx tool to reach a .top files to run
simulations. I tried to separate in different "chains" the "pieces" of the
protein after removing the K, later I joined the XXXX residue in the holes
that I made. I insert the .itp of the XXXX residue in .top file, the
problem is that when I run grommp there are different numbers of atoms in
final .pdb and final .top (Fatal error), this is due to that I needed to
remove some H to join the XXXX residue to a specific place. Is there
somebody to help me? How I can obtain a final .pdb file with a
correct .top?

Thanks in advance

Vicente Dominguez-Arca

PhD Candidate in Applied Physics
Biophysics and Interfaces Group
University of Santiago de Compostela
SPAIN