[gmx-users] Re: 1-4 cut off error during EM

[bharat gupta]

thanks..

On Fri, Jun 24, 2011 at 11:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> ok after reading the documentation, I think the problem is with the ligand
>> topology or parameter. For that  I need to simulate the structure in vacuo
>> to check for any unusual changes in topology ...
>>
>
> A topology is a static entity; nothing about it changes.  An in vacuo EM of
> the protein and/or the modified residue itself would be a reasonable start
> to diagnosing the underlying problem.
>
> -Justin
>
>  On Fri, Jun 24, 2011 at 11:23 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    bharat gupta wrote:
>>
>>        Hi,
>>
>>        I generated the topology and parameter file for phosphotyrosine
>>        usin Swiss param and during minimization, it's giving 1,4 cut
>>        off error. I found that the cut off for 2 paris of atom is more
>>        than the default value. So, in that what shall I do??
>>
>>
>>    http://www.gromacs.org/__**Documentation/Errors#1-4___**
>> interaction_not_within_cut-off<http://www.gromacs.org/__Documentation/Errors#1-4___interaction_not_within_cut-off>
>>    <http://www.gromacs.org/**Documentation/Errors#1-4_**
>> interaction_not_within_cut-off<http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off>
>> **>
>>    http://www.gromacs.org/__**Documentation/Terminology/__**Blowing_Up<http://www.gromacs.org/__Documentation/Terminology/__Blowing_Up>
>>    <http://www.gromacs.org/**Documentation/Terminology/**Blowing_Up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
>> >
>>
>>    Note that this error is incredibly common and you can probably find
>>    thousands of similar posts in the list archive (hint: search the
>>    archive).  Most errors are described in the "Errors" page above
>>    (hint: there's lots of information on the Gromacs site, so always
>>    check there whenever you have a problem).
>>
>>    -Justin
>>
>>        --         Bharat
>>        Ph.D. Candidate
>>        Room No. : 7202A, 2nd Floor
>>        Biomolecular Engineering Laboratory
>>        Division of Chemical Engineering and Polymer Science
>>        Pusan National University
>>        Busan -609735
>>        South Korea
>>        Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>        Mobile no. - 010-5818-3680
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>>        <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
>>
>>
>>
>>    --     ==============================**__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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