[gmx-users] Proper and improper from other ff?

[Justin Lemkul]

On 3/22/13 3:14 PM, 라지브간디 wrote:
>
> 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 ?
>

Different force fields derive and implement parameters in different ways.  Hence 
why it makes no sense to try to combine them.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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