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 <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 >> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@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-requ...@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 : monu46...@yahoo.com
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