Thanks Justin, Chris, I will give it a try and follow what you suggested.
Cheers Mohsen On Tue, Jun 14, 2016 at 2:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/14/16 2:04 PM, Christopher Neale wrote: > >> You might see if CHARMM_GUI has parameters for it. This is not to say that >> they will be amazing parameters, as I have not looked into their approach >> to >> generate parameters and it may well be rational cut and paste, but they do >> have parameters for loads of lipids. If they don't have parameters, you >> might >> also consider asking them to put your HG on their to-do list. My >> understanding is that they want to add useful moieties. >> >> > CHARMM-GUI has access to the full CHARMM force field, and the full > complement of every lipid parametrized for it (which is indeed quite > extensive). If a particular molecule (lipid type) is missing, it will call > ParamChem (the CGenFF program's web server) to generate a topology for the > full molecule. As I said in my first reply, this would be suboptimal as > most of the necessary parameters will already be in the highly optimized > CHARMM36 lipid force field. Without knowing what the OP wants to work > with, it's hard to say further, but I expect most of the work will already > be done, and one needs to address a suitable model compound or two to work > out any new linkages. > > -Justin > > > Chris. >> >> ________________________________________ From: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mohsen >> Ramezanpour <ramezanpour.moh...@gmail.com> Sent: 14 June 2016 13:53:26 >> To: >> Discussion list for GROMACS users Subject: [gmx-users] Lipid >> parameterization >> >> Dear Gromacs users, >> >> I am trying to parameterize a lipid molecule with a weird headgroup :-) in >> Charmm36 force field for doing simulation in GROMACS. Reading through >> literature, I found that Swissparam, and Paramchem.org are two useful >> tools >> to make the topology files automatically. >> >> However, both seems to be suitable for small drug-like molecules than >> large >> biological molecules, like lipids. Swissparam is a mixture of charmm >> parameters and MMFF and is not based on any specific CHARMM FF version. >> Paramcharm has also recommended to not use it for biological molecules. >> >> Although lipids are biological molecules, but I was wondering what will >> happen if we consider the "whole synthetic lipid" as a drug-like molecule. >> >> >> In this case, we might be able to mix it with other lipids which have been >> parameterized in Charmm36? >> >> Thanks in advance for your comments Cheers Mohsen -- *Rewards work better >> than punishment ...* -- 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. >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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. > -- *Rewards work better than punishment ...* -- 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.
