[gmx-users] Is it possible to generate lipid.itp with Charmm36 ff?

[Justin Lemkul]

On 4/7/15 4:44 PM, Yunlong Liu wrote:
> Oh I see. I saw the website this afternoon. Do you refer to the package
> charmm36-nov2014? I checked the file inside but see no dppc or popc entry
> inside. I just want to make sure whether it can work for popc membrane?
>

Yes.

> I ask this since I don't quite understand how the lipid membrane force field
> top files should be correctly represented in GROMACS. I read your tutorial
> and see you are talking about "lipid.itp".
>

Different force fields, different approaches.  I would encourage you to follow 
Micholas' advice and proceed through CHARMM-GUI.  It will even build the entire 
membrane for you if you want, as well as provide all of the inputs (.mdp) with 
correct settings (including things that people frequently screw up).

We don't provide individual molecule .itp files for lipids.  They are all .rtp 
entries, so you can process the structure directly with pdb2gmx.

-Justin

-- 
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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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