Thanks Peter. :-) Sincerely, Shima
----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, September 24, 2012 6:26 PM Subject: Re: [gmx-users] packing lipids What does trace show? (Trace is supposed to draw a vertex between each alpha carbon). VMD has no knowledge of connectivity, it can only draw bonds through distance calculatoin between consecutively numbered atoms. Perhaps there is a misnumbering of the .gro file. On 2012-09-24 07:48:17AM -0700, Shima Arasteh wrote: > > > In fact, the structure visualized by VMD and choosing line as draw style is > ok, but the second structure of protein ( I mean the choosing ribbons) shows > a broken structure. How come? what does it mean? > > Thanks in advance. > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Monday, September 24, 2012 2:09 PM > Subject: Re: [gmx-users] packing lipids > > > > On 9/24/12 6:22 AM, Shima Arasteh wrote: > > > > Dear gmx users, > > > > Is it possible that the protein got broken during shrinking iteration of > > packing lipids around the protein? > > > > Only if it were broken to begin with. This is a rather vague statement; if > you > need further help, you will have to be a lot more specific about what's going > on. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > * Please search the archive at > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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