Re: [gmx-users] Glycoproteion MD
Dear (sorry cant read chinese), You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites. That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either the CRC or national institute of standards) for a small subset of sugars, inclusive of the inter-chain bonds, and then just use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for phosphorylated to sugar, etc... as inclusive this would only be several to a dozen atom types or somthing)(then you can post it :-))...but it might be easier than trying to define things based on single sugar moieties available on the web, as you most likely would have errors when your suger moities are large from the inter-sugar bonds between subunits, such as a 10-20 length polysacharide on a glycosylated protein. This is less trivial than it might seem, but would still take a few days, and you might be able to use all but say 1-2 atoms if you find several defined parameters for sugars on the web already... Sincerely, Stephan Watkins Original-Nachricht Datum: Fri, 31 Aug 2012 09:26:38 +0800 Von: 陈应广 525342...@qq.com An: gmx-users gmx-users@gromacs.org Betreff: [gmx-users] Glycoproteion MD 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. Thanking all -- gmx-users mailing listgmx-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] Glycoproteion MD
Thanks for your help ,you can call me Guang.I come from China. -- -- ??: lloyd riggslloyd.ri...@gmx.ch; : 2012??8??31??(??) 7:25 ??: Discussion list for GROMACS usersgmx-users@gromacs.org; : Re: [gmx-users] Glycoproteion MD Dear (sorry cant read chinese), You can find some OPLS or 53a6 Parameters on the web by doing extensive searches, mostly they are free, but hosted on varied individual lab web sites. That, or it may be easier to define some sets of bonds (angles, dihedrials, lengths charges, etc...from either the CRC or national institute of standards) for a small subset of sugars, inclusive of the inter-chain bonds, and then just use the defined names you gave the sugar atoms (ie Cc for sugar carbon, Pc for phosphorylated to sugar, etc... as inclusive this would only be several to a dozen atom types or somthing)(then you can post it :-))...but it might be easier than trying to define things based on single sugar moieties available on the web, as you most likely would have errors when your suger moities are large from the inter-sugar bonds between subunits, such as a 10-20 length polysacharide on a glycosylated protein. This is less trivial than it might seem, but would still take a few days, and you might be able to use all but say 1-2 atoms if you find several defined parameters for sugars on the web already... Sincerely, Stephan Watkins Original-Nachricht Datum: Fri, 31 Aug 2012 09:26:38 +0800 Von: ?? 525342...@qq.com An: gmx-users gmx-users@gromacs.org Betreff: [gmx-users] Glycoproteion MD 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. Thanking all -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Glycoproteion MD
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 listgmx-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
Re: [gmx-users] Glycoproteion MD
Hi Guang, You can use the GLYCAM force field, which has parameters for carbohydrates and glycoproteins compatible with AMBER99. You can get the AMBER topology and structure files directly from their web interface, the Online Glycoprotein Builder ( http://glycam.ccrc.uga.edu/ccrc/gp/ http://glycam.ccrc.uga.edu/ccrc/), and them convert it to .top and .gro with the acpype script. I've done it sometimes. I hope it is helpful for you. best regards, Leandro 2012/8/30 陈应广 525342...@qq.com 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. Thanking all -- gmx-users mailing listgmx-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 listgmx-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] Glycoproteion MD
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. Thanking all-- gmx-users mailing listgmx-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
Re: [gmx-users] Glycoproteion MD
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 listgmx-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] Glycoproteion MD
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. Thanking all-- gmx-users mailing listgmx-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
