Hi, If you can't find parameters for glycoprotein's MD for charmm27, OPLS or Amber99 (and GROMOS is an alternative for you), we've been working on MD simulations with this class of biomolecules, using GROMOS96 43A1 force field, as described:
Pol-Fachin, L.; Fernandes, C.L.; Verli, H.: GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations. Carbohydrate Research 344 (2009) 491–500. Fernandes, C.L.; Sachett, L.G.; Pol-Fachin, L.; Verli, H.: GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydrate Research 345 (2010) 663–671. Best regards, Laércio Pol-Fachin --------------------------------------------------------------------- Message: 1 Date: Thu, 30 Aug 2012 21:32:00 -0400 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Glycoproteion MD To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <50401410.7070...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed On 8/30/12 9:26 PM, 陈应广 wrote: > Dear all I am interested in simulating a model of Glycoproteion. I could'nt > find the define of the residue in any forcefield .rtp file of GMX. I am using > Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for > charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where > else I should search for these. > If they haven't already been derived (and thus likely published), then you'll have to derive them yourself in a manner consistent with the original force field. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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
