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

[Thomas Piggot]

Hi Carlos,

You can make one very easily yourself by taking a pdb of one CHARRM36 
POPC lipid and using pdb2gmx. You only then need to make very minor 
modifications to convert the .top into an .itp.

Cheers

Tom

On 12/14/2014 08:58 PM, Carlos Navarro Retamal wrote:
> Dear Tsjerk,
> Could you please send me the popc.itp file for chamm36 forcefield?
> If you have any troubles with my institutional email account, try to my gmail account (it is on my signature)
> Best regards,
> Carlos
>
>
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
>
> On Saturday, December 13, 2014 at 12:49 PM, Carlos Navarro Retamal wrote:
>
>> Hi everyone,
>> First of all thanks to both of you for your quick replies.
>> Dear Tsjerk,
>> I’ll be much appreciated if you could send me the *itp file of POPC.
>> Thanks a lot,
>> Carlos
>>   
>> --
>> Carlos Navarro Retamal
>> Bioinformatic engineer
>> Ph.D(c) in Applied Science, Universidad de Talca, Chile
>> Center of Bioinformatics and Molecular Simulations (CBSM)
>> Universidad de Talca
>> 2 Norte 685, Casilla 721, Talca - Chile
>> Teléfono: 56-71-201 798,
>> Fax: 56-71-201 561
>> Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
>>   
>>   
>> On Saturday, December 13, 2014 at 12:21 PM, Tsjerk Wassenaar wrote:
>>   
>>> 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 (mailto: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 (mailto:jalemkul at outerbanks.umaryland.edu) | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>   
>>>> ==================================================
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-- 
Dr Thomas Piggot
University of Southampton, UK.