Thanks Justin. I would also like to know the reliability of parameters generated using swiss param.
On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > >> Thank you Mark and Justin. >> Now, I have carried out simulations using PME electrostatics and using >> all other >> parameters (except gromos 96 43a1 ff used) as suggested in >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/lysozyme/ >> >> The protein is not loosing its structure now. But the problem is if I >> carry out >> simulations in the presence of experimentally known stabiliser generated >> using >> ProDrg (keeping all the parameters same while simulating both in the >> presence >> and absence of stabiliser), the partial loss of secondary structure is >> observed >> in the presence of stabilizer relative to the case in its absence at 350K >> thereby implying simulations going against experimental observations >> (although >> slight stabilization was observed at 300K). Simulations were repeated >> twice with >> two different force fields. >> However if I use above em,pr,full parameters with cut-off electrostatics, >> although secondary structure is lost in the initial stages but I could >> clearly >> see the stabilization behaviour of additive in terms of secondary >> structure >> retainment till longer time. Is this observation a matter of chance- >> reliable or >> not? What could be the possible reason for not observing such >> stabilization with >> better parameters? >> >> > Cutoff electrostatics are horribly inaccurate. The fact that you > conveniently see what you hope to when using a plain cutoff is likely by > chance. > > The bigger issue is the use of PRODRG parameters. As I have said numerous > times on this list, the parameters it produces are demonstrably inaccurate > and require reparametrization. > > http://pubs.acs.org/doi/abs/10.1021/ci100335w > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.