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

[Tsjerk Wassenaar]

Hey,

The all atom mapping of Martini to CHARMM36 is available in
backward/initram, so the conversion can be done directly. You only need to
have a CHARMM36 POPC itp file. I can provide one if needed.

Cheers,

Tsjerk
On Dec 13, 2014 3:38 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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