[gmx-users] Lipid parameterization

[Mohsen Ramezanpour]

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 <jalemkul at 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-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
>>
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> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
*Rewards work better than punishment ...*