[gmx-users] [ bondedtypes ]

[Justin A. Lemkul]

Lara Bunte wrote:
> Hi
> 
> The first part in a .rtp file is the [ bondedtypes ] with syntax
> 
> [ bondedtypes ]
> ; bonds    angles    dihedrals    impropers
>      1             1              1                 2
> 
> 
> 
> 1.)
> 
> What do this numbers mean? I found nothing in the manual to that. 
> 

They are the function types for these different interactions.  Function types 
are listed in Table 5.5.

> 
> 
> 2.)
> If you have improper dihedrals, do you really nead both in this section? Why not only impropers? 
> 

The order of the function types must be adhered to so that the parameters are 
properly interpreted.  Check gmx.ff/aminoacids.rtp for a complete description of 
each of the 8 possible columns and the order that they must follow.

-Justin

-- 
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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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