[gmx-users] Re: Problem in Disulfide Bond

[parthiban at ncbs.res.in]

> 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>
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> 	<AANLkTin5r=+mn5edW=ZqdhRu8fAcoQEdoViXC8X28StC at mail.gmail.com>
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>
> 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.

> ------------------------------
>
> 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>
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>
>
>
>> > 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.