[gmx-users] Question for Gromacs Users

[Kroon, P.C.]

This is a known bug in Martinize; you applied the correct fix.
And Justin is right, it would have been better to post this kind of
question on the Martini forum (www.cgmartini.nl); I'm also rather sure that
this answer is on there somewhere.

Peter

On Tue, Apr 12, 2016 at 8:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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