[gmx-users] Re: Automated Topology Builder job partially completed

[Justin A. Lemkul]

On 6/9/12 10:30 AM, James Starlight wrote:
> Justin,
>
> I have also question about inclussion of the part of the topology file wich was
> done by the external server ( e.g by ATB) in the topology of my molecule.
>
> E.g I'm working with GFP wich include non-standart chromophore group wich is
> covalent bonded to the all protein. So I've extracted chromophore only from my
> GFP and done it parametrisation by ATB. What is the easiliest way to include
> this new topology as well as part of the molecule back to the whole GFP?
>

The only way to do it:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-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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