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

[Justin A. Lemkul]

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/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
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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://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

========================================