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

[bharat gupta]

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 ...

On Fri, Jun 24, 2011 at 11:23 AM, Justin A. Lemkul <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/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
>> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110624/6763f1e7/attachment.html>