Hey Julio, Shine, I would like to see the 'here' and 'here'. Pymol has two routines for determining secondary structure, one of which uses the same approach as dssp to classify helices and sheets. A relevant question is, what is a helix? Is a helix a stretch of residues that is defined by dssp as helix? That is also just a heuristic. Justin is quite right that what is observed is largely the consequence of the force field and settings. Make sure that the force field and settings you use reproduce proper behaviour. The structure will not just change because of the placement of waters, or that shouldn't be a persistent effect. And why would it be a helix for all of the residues for all of the time? Because the crystal structure shows it's a helix? Maybe it's more flexible in solution and only a helix for a given proportion of time. If you're afraid to see (temporary) loss of structure, then it may be better not to simulate at all.
Cheers, Tsjerk On Fri, Dec 14, 2012 at 6:32 AM, Julio Dominguez <achero...@hotmail.com>wrote: > Hello Shine, > > Besides what Justin mentioned you have to be careful of what you consider > a helix or a loop. Pymol is note very accurate when it assigns secondary > structure. I recommend you install dssp within Pymol (see here and here) > and double check you secondary structure. Odds are that it still is a helix. > Best regards. > > Message: 4 > > Date: Thu, 13 Dec 2012 22:53:30 +0530 > > From: Shine A <shin...@iisertvm.ac.in> > > Subject: [gmx-users] conformational change > > To: gmx-users@gromacs.org > > Message-ID: > > <CAEUDBJr1nBB2We-rJzg0H9er9Bf0cEgqn4mgwratJyPff=A0= > g...@mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Sir, > > > > I am studying the dynamics of a beta barrel shaped membrane > > protein. The starting end of the barrel is a helix which is inside the > > barrel. During salvation with genbox some water molecules entered inside > > the barrel.Then I did the 20 ns dynamics.After dynamics more number of > > water molecules trapped inside the barrel. I convert the output gro file > > into pdb and viewed using pymol. Then I noticed that the starting helix > > part is changed in to loop.Then I calculated the rmsd deviation and > radius > > of gyration, it not showing any characteristic deviation.Is water > molecule > > change the conformation of helix inside the barrel? Is it necessary to > > delete all the water molecules inside the barrel before dynamics? then > > how? > > > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
