[gmx-users] Protein-DNA simulation LINKS error

[Justin Lemkul]

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?

> 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.

-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

==================================================