[gmx-users] Question for Gromacs Users

[Justin Lemkul]

On 4/12/16 2:22 PM, Brier, Troy wrote:
> 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
> 0.39nm/5000kJ/mol.
>
> 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
>
> to:
>
>   (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?
>

The wording of the error message states that it's supposed to be a constraint 
(i.e. fixed distance), not a harmonic interaction.  So if it's a constraint, 
it's simply being written to the wrong section of the topology.  It may be 
better to post this question to the MARTINI forum.  A difference between a rigid 
0.24 nm distance and a harmonic 0.39 nm distance is quite substantial.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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