[gmx-users] Problem Simulating a protein with small peptides

Arash Firouzbakht arashfirouz at gmail.com
Thu Dec 18 13:21:05 CET 2014

Dear GROMACS experts,

I am simulating a protein with a number of KVV tripeptides, using run
parameter files in GROMACS tutorial website(Dr. Justin Lemkul) with
changing JZ4 to KVV and changing temperature to 310K.

After I add the KVV coordinate file(KVV.gro, attached) to the protein box
and further solvate it, the output .gro file seems to be OK. But once I
subject it to the genion command to neutralize the charge the output
coordinate file changes ! All KVV residues change to their subresidual
names which are recognized by the software as LYS-VAL-VAL. I need GROMACS
to recognize the tripeptides with their former name.
I attached part of the problematic .gro file containing KVV coordinates.

How can I solve this issue?
Thanks in advance

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