[gmx-users] adding hydrogen atoms into a POPC membrane

[Justin Lemkul]

On 12/13/14 12:47 AM, Carlos Navarro Retamal wrote:
> Dear gromacs users,
> I just ran a CG simulation of a system consisting in a protein embedded in a POPC membrane solvated in water.
> After that i ran the script .initram to obtain an AA representation of my system (gromos54a7), but sadly i couldn’t find a *.itp with the description of the hydrogen atoms of the membrane.

Gromos96 54A7 is not all-atom, hence why the hydrogens are "missing."

> So, is there a way to add the missing atoms after this step? and if its not posible, could someone provide me with the ‘correct’ *itp file (hopefully gromos or charmm ff) ?

We include POPC in our CHARMM36 port, but you'll need to add an .hdb entry for 
POPC, which is largely very repetitive but very easy.

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

-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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