[gmx-users] Capping residues

[Sai Pooja]

Would it be possible to add some capping residues (like --COCH3 and --NHCH3)
by writing a separate .itp file and including it in the topology file? Is
there a way to make it consistent with charmm forcefield?

Can this be done alternatively by modifying the .rtp file? If yes, what
other operations must one do before using these .rtp files?

On Wed, Jun 30, 2010 at 8:39 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Date: Thursday, July 1, 2010 9:58
> Subject: Re: [gmx-users] Capping residues
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> >
> >
> > Sai Pooja wrote:
> > >Hi,
> > >
> > >1) What capping residues are recognized by charmm implemented
> > on gromacs in the latest git version?
> >
> > It looks like there aren't any.  Check the .rtp file to be sure.
>
> There aren't. I had a discussion with Par Bjelkmar a while back about
> including some, but I don't recall the outcome.
>
> Mark
>
>
> > >I was trying to use ACE for acetyl but it is not recognized by
> > pdb2gmx.>
> > >
> > >2) Is it possible to define caps at residues other than those
> > at the termini?
> > >
> >
> > What exactly do you consider a cap?  Usually a capping
> > residue is applied only to N- and C-termini.  If you're
> > trying to make some sort of modified sidechain, then you have to
> > look into parameterizing it yourself.
> >
> > http://www.gromacs.org/Documentation/How-tos/Parameterization
> >
> > -Justin
> >
> > >Regards
> > >Pooja
> > >
> > >--
> > >Quaerendo Invenietis-Seek and you shall discover.
> > >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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-- 
Quaerendo Invenietis-Seek and you shall discover.
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