Show us that part of your topology. When you used ffamberports have you renamed the CYS to CYS2? <br><br>Oliver<br><br><div class="gmail_quote">On 20 January 2011 09:23, <span dir="ltr"><<a href="mailto:parthiban@ncbs.res.in">parthiban@ncbs.res.in</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">> Message: 5<br>
> Date: Wed, 19 Jan 2011 08:37:20 -0500<br>
> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4D36E910.6030106@vt.edu">4D36E910.6030106@vt.edu</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<div class="im">><br>
><br>
><br>
> <a href="mailto:parthiban@ncbs.res.in">parthiban@ncbs.res.in</a> wrote:<br>
>> Hi<br>
>><br>
>> I am using a dimer for my simulation system which is connected by 2<br>
>> disulfide bonds.<br>
>> After energy minimization for even few cycles, the disulfide bond breaks<br>
>> which is not expected.<br>
><br>
> Bonds do not break in classical molecular mechanics. One of two things is<br>
> happening:<br>
><br>
> 1. There was never a bond to begin with (check your topology)<br>
</div>There do a bond exists.<br>
<div class="im">> 2. The bond is highly strained, in which case something is wrong with your<br>
> structure.<br>
><br>
>> i have applied amber99 force field and prepared the system. while i<br>
>> tried<br>
>> with another force field in Gromacs which did not worked at all.<br>
><br>
> What does that mean? What failed?<br>
</div>As said previously the bond is strained only after pdb2gmx itself. is<br>
there any other way to fix it.<br>
<br>
but in gendral the molecule is free from strains.<br>
<div class="im">><br>
>> also i have tried by editing specbond.dat as well but of no use.<br>
><br>
> In what way? Have you seen the information at:<br>
><br>
> <a href="http://www.gromacs.org/Documentation/File_Formats/specbond.dat" target="_blank">http://www.gromacs.org/Documentation/File_Formats/specbond.dat</a><br>
><br>
<br>
</div>i tried to alter the distance of cys bond length by +/-.<br>
reg,<br>
Parthi.<br>
<div class="im"><br>
> -Justin<br>
><br>
>> can any one share/discuss some ideas how to fix this.<br>
>><br>
>> reg's,<br>
>> Parthiban.<br>
>><br>
<br>
<br>
--<br>
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