[gmx-users] Protein-DNA simulation LINKS error

[Erik Marklund]

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.

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?
>> 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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