[gmx-users] Protein-DNA simulation LINKS error

[Erik Marklund]

> On 24 Jun 2015, at 10:58, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 6/24/15 5:20 AM, Erik Marklund wrote:
>> Hi Timofey,
>> 
>> If I recall correctly, there is no constrainttype defined for the pair MCH3 CT in ffbonded.itp, which is needed for making a 4out virtual site for the methyl group in thymine. You need to work out the geometry that yields the correct moment of inertia for the methyl group and define a constraint type accordingly.
>> 
> 
> There are virtual sites in this system?  I saw no mention of this; have I missed something?

Perhaps presumptuous of me to assume that.

> 
>> Kind regards,
>> Erik
>> 
>> 
>>> On 24 Jun 2015, at 06:38, Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:
>>> 
>>> 
>>> I have ordinary DNA and an oxoguanine site? What actions should I take to correct these vsite parameters?
> 
> If you're using virtual sites, back up and don't do that.  Solve simple issues before doing harder things.  If you have a non-standard residue like 8-oxoG, then perhaps its parameters are insufficient.  Try running with a "normal" DNA (e.g. G instead of 8-oxoG) and see if that works first, before doing something atypical.
> 

I agree with Justin. Make sure you have a working protocol for normal DNA, then one for the modified nucleotide.

Erik

> -Justin
> 
>>>> Message: 1
>>>> Date: Tue, 23 Jun 2015 22:24:20 +0000
>>>> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
>>>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>>>> Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
>>>> Message-ID: <61EDBF38-6D1F-4089-8EBE-03CAAAFF6F14 at chem.ox.ac.uk>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>> 
>>>> The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have.
>>>> 
>>>> Erik
>>>> 
>>>>> On 23 Jun 2015, at 21:15, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>> On 6/23/15 7:13 AM, Timofey Tyugashev wrote:
>>>>>> I'm trying a few simulations of a enzyme-DNA complex and while in short
>>>>>> timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation
>>>>>> crashes with numerous LINCS warnings.
>>>>>> Maybe there are some errors in mdp configuration file? To mine inexperienced eye
>>>>>> they look good enough.
>>>>>> I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box,
>>>>>> system requires around 30 Na atoms to compensate the charge. I also create a
>>>>>> combined group Protein_DNA using make ndx.
>>>>>> Here are the MDPs:
>>>>>> 
>>>>>> Ions: http://pastebin.com/xCUqiDM0
>>>>>> EM: http://pastebin.com/WcXdXBWf
>>>>>> NVT: http://pastebin.com/sdVqfGDM
>>>>>> NPT: http://pastebin.com/AsMVC7yH
>>>>>> MD: http://pastebin.com/sne7Fpzt
>>>>>> 
>>>>>> Any help?
>>>>> AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not necessarily to blame for the crash.  In general, here's the usual troubleshooting protocol:
>>>>> 
>>>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>>>>> 
>>>>> -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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>> 
> 
> -- 
> ==================================================
> 
> 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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