[gmx-users] Proper and improper from other ff

[Justin Lemkul]

On Saturday, March 23, 2013, 라지브간디 wrote:

> Thanks for your reply.
> Except charmm27 in gmx, all the ff fails to describe the angle, bonds and
> dihedral of heme ligated proteins. Also, Chamm27 also couldnt do for heme
> interacts with histidine part. Hence I've utilized the parameter details
> from articles. Only I am missing how do I describe the torsion angle
> details to this particular heme ligand part. Is that okay if I avoid the
> torsion ?
>
> Hope you understand what I mean in here.
>
>
>
Simulations of heme-containing proteins are fairly common. Certainly
someone will have published a complete parameter set. Mixing force fields
and ignoring energy terms are not sensible.

-Justin


>
> > Different force fields derive and implement parameters in different
> ways. Hence
> why it makes no sense to try to combine them.
> > Dear Justin,
> >
> > Actually I've manually added the heme -ligand parameters details such as
> bond, angle and dihedral to my topology created by pdb2gmx via gromos43a1.
> ( Those manually added parameters details are taken from charmm and amber
> ff, which are available in some published articles ).
>
> If you're doing this, you're creating a hybrid force field that makes no
> sense.
> There are parameters for heme within Gromos96 already; why are you making
> these modifications?
>
> > I confused while interpreting the improper values from those published
> article where they both shown (amber and charmm) improper in X (generic
> indicator) way, whereas the gromos improper values for atoms are in direct
> way by not using X generic indicator.
> >
> > Is that improper details are important for heme-ligand case ? If so, how
> do I make them favor to gromos by this article values ?
> >
>


-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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