[gmx-users] Question for Gromacs Users

Brier, Troy briert1 at tcnj.edu
Tue Apr 12 20:39:33 CEST 2016

To whom it may concern,

I am attempting to run a single protein in water Martini coarse grain
simulation. I used martinize.py (version 2.4) to coarse grain the
protein and add a dilsulfide bond. When attempting to run the
minimization phase (I am using Gromacs version 5.1) I receive the
following error:

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For
more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors

After troubleshooting I determined the error came from the Bonds
section in the Protein_A.itp file produced from martinize.py, and
specifically from the section having to do with the disulfide bonds.
The error seems to be related to martinize.py determining the bond
constraints of the disulfide bone to not match those of the literature
values, and the script prints the following message:

Note: Cysteine bonds are 0.24 nm constraints, instead of the published

So I changed the section in the Protein_A.itp file from:

(Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
  253   281      1   0.24000


 (Error Causing  Protein_A.itp file under [bonds])
; Links/Cystine bridges
  253   281      1   0.39000 5000

and then the minimization step runs without the fatal error. What I
would like to know if making this change is the proper thing to do or
should I keep the constraint distance at 0.24 nm and just add in the
bond strength of 5000 kJ/mol?

Thanks for your help,

Troy Brier

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