[gmx-users] Lipid parameterization

[Christopher Neale]

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.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mohsen Ramezanpour <ramezanpour.mohsen at 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-request at gromacs.org.