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

[Carlos Navarro Retamal]

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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