[gmx-users] Re: Problem in Disulfide Bond

[Justin A. Lemkul]

parthiban at ncbs.res.in wrote:
>> Message: 3
>> Date: Thu, 20 Jan 2011 09:30:00 +0000
>> From: Oliver Grant <olivercgrant at gmail.com>
>> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID:
>> 	<AANLkTin5r=+mn5edW=ZqdhRu8fAcoQEdoViXC8X28StC at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Show us that part of your topology. When you used ffamberports have you
>> renamed the CYS to CYS2?
>>
>> Oliver
>>
> 
> could you explain this in detail where this change have to done.? i can
> check again.
> 

If the disulfide was created by pdb2gmx, then specbond.dat will have done this 
for you and assigned the proper parameters.  Did pdb2gmx automatically assign 
your bond for you, or did you make post-pdb2gmx manual changes to your topology?

-Justin

>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 20 Jan 2011 20:54:39 +1100
>> From: Mark Abraham <mark.abraham at anu.edu.au>
>> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <7690be842aff.4d38a10f at anu.edu.au>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>>
>>>> parthiban at ncbs.res.in wrote:
>>>>> Hi
>>>>>
>>>>> I am using a dimer for my simulation system which is connected by 2
>>>>> disulfide bonds.
>>>>> After energy minimization for even few cycles, the disulfide bond
>>> breaks
>>>>> which is not expected.
>>>> Bonds do not break in classical molecular mechanics.  One of two
>>> things is
>>>> happening:
>>>>
>>>> 1. There was never a bond to begin with (check your topology)
>>> There do a bond exists.
>>>
>> So you can see in your [bonds] section an entry for the two atom numbers?
> 
> I cant see any corresponding entry with res.to CYS residues.
> 
>>
>>>> 2. The bond is highly strained, in which case something is wrong with
>>> your
>>>> structure.
>>>>
>>>>> i have applied amber99 force field and prepared the system. while i
>>>>> tried
>>>>> with another force field in Gromacs which did not worked at all.
>>>> What does that mean?  What failed?
>>> As said previously the bond is strained only after pdb2gmx itself. is
>>> there any other way to fix it.
>>>
>> Previously you said the bond was strained after EM. pdb2gmx is not capable
>> of straining a bond.
>>
>> Be sure you are not looking at "bonds" generated via heuristics in some
>> visualization program. If pdb2gmx is generating a disulfide bond, it will
>> say so in the standard output, and you will be able to find it in the
>> [bonds] section. Otherwise, there is no bond.
>>
>> Mark
>>
> 
> I used pymol and vmd to visualize this
> 
> Thanks
> Parthiban.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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