Warnings and Errors in pdb2gmx and grompp

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Dear GROMACS users,

Though these problems have been discussed earlier, I would like to raise this topic again as the solutions seem confusing to me. I am new to GROMACS and facing multiple issues while preparing a system of protein in

spce water, much like the lysozyme tutorial, but using the GROMOS54a7 force field

(instead of OPLS/AA).

  1. For step 1: While using pdb2gmx to generate a .gro file, I get the following


Duplicate line found in or between hackblock and rtp entries.

I came across an archived mail that says these warnings arise due to some

typo in the ff.itp file. However, I have not tampered with the files that are

present in the gromacs library so any explanation as to what can be the source

of these warnings will be most helpful.

  1. The pdb2gmx step terminates with “successful” creation of the topology file.

However on closer inspection, I found out that certain fields corresponding to

bonds, angles and dihedrals are empty.

For bonds: The field corresponding to parameter c0 is missing for the 4 S-S bonds

present in my protein.

For angles: The field corresponding to parameter c0 is missing for the 4

CH2-S-S bond angles.

For dihedrals: The field c0 is absent for






The next two steps involving solvation proceeds smoothly but the ion addition

step terminates with the following error:

No default Proper Dih. types

I tried the same process with the lysozyme tutorial which is well documented

but instead of OPLS/AA I opted for the GROMOS54a7 force field and ended up

with the same kind of errors. Previous solutions suggest to fill the empty fields

by hand but I am not sure as to how to obtain these parameters, specially for the

dihedrals where two amino acids are involved.Any suggestion regarding this is most