[gmx-users] Protein-DNA simulation LINKS error

[Justin Lemkul]

On 6/24/15 7:41 AM, Timofey Tyugashev wrote:
> 24.06.2015 15:58, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 24 Jun 2015 05:58:47 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
>> Message-ID: <558A7F57.7000606 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> 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
> I haven’t planned to use virtual sites for this simulations yet. A short
> calculation with normal guanine worked fine, one with longer time is still in
> queue for calculation, so I'll definitely check it later.
> Looking through the literature I've encountered different cutoff values, mainly
> from 1.0 to 1.4 for forcefields, so I simply picked the middle one of 1.2. How
> bad it is?

Read the AMBER99sb-ILDN paper.  Use those values.  You can't pick some arbitrary 
value in the ballpark of what different models use.  That doesn't make sense. 
Cutoffs are part of the force field; treat them as such.

Your problem almost certainly comes from an inaccurate 8-oxoG topology if normal 
guanine works fine.

-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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