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 <jalem...@vt.edu
<mailto:jalem...@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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E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com <mailto:monu46...@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 : monu46...@yahoo.com <mailto:monu46...@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
========================================
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