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

[Carlos Navarro Retamal]

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 or 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
> >  
> > ==================================================
> > --
> > Gromacs Users mailing list
> >  
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >  
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >  
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org (mailto:gmx-users-request at gromacs.org).
> >  
>  
> --  
> Gromacs Users mailing list
>  
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>  
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org (mailto:gmx-users-request at gromacs.org).
>  
>