Hi all, I've had problems before with waters placed within a beta-sandwich protein by genbox. Although it is theoretically a matter of running the simulation and waiting for the waters to "come out", in practice this took about 30 ns and destroyed a considerable amount of the beta-strands.
The solution I found at the time was to use a bigger box and to remove a shell of waters which were at a distance of 5 or less angstroms from the protein. Then I did a very short (~100ps) NPT equilibration with position restraints applied to the protein atoms. During this "solvation simulation" the waters solvated the protein, the box shrank and the density increased to the "normal" averages. I found that by doing this the waters enter the cavities in a much more "natural" way. So, Shine, maybe doing this can help you, if the inner waters are related to the helix destabilization. I used VMD to get the residue numbers of the waters from the .gro file of the whole system (there were some issues with pymol), then I removed such residues from the .gro file of the box and adjusted the topology accordingly. I hope it helps, Leandro Bortot 2012/12/14 Julio Dominguez <achero...@hotmail.com> > Morning Shine and Tsjerk, > Sorry for the missing links (here and here), I was refering to PyMol > wiki's and a blog: > http://macosxpostdoc.blogspot.mx/2012/04/dssp-through-pymol.html > http://www.pymolwiki.org/index.php/DSSP_Stride > But what Tsjerk mentions is far more relevant, I was thinking statically > last night. First off, PyMol automatic secondary structure detection is > spotty. Second, the command dss within PyMol does a better job. Third, the > most systematic way to visualize secondary structure within Pymol would be > to use DSSP (or Stride) within PyMol. > Thinking dynamically, you could run do_dssp, part of Gromacs, and check > the time course of the whole secondary structure during your simulation. > There is also g_helix, which can output the % of time a structure spends as > a helix. > As everybody has pointed out, the forcefield is the most probable cause. > Be sure to check recent literature to make sure the ff you are using is not > biased against (or in favor) of helical structures. > Best regards. > > > > Message: 4 > > Date: Fri, 14 Dec 2012 09:50:28 +0100 > > From: Tsjerk Wassenaar <tsje...@gmail.com> > > Subject: Re: [gmx-users] conformational change > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: > > <CABzE1Sh7pr6yYhQfn2ghhdKAcpW2Q_KRgEzrPjNJD= > qjjnm...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > 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. > > -- > 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