Sv: Re: [gmx-users] Add bridging residue

[Justin A. Lemkul]

Edvin Erdtman wrote:
>> "Justin A. Lemkul" wrote: Please see the following: 
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>> 
> 
> Yes. I know all that! But my question was if there is a possibility to build
> a new residue which has a cross-link bond to another residue. How can I
> define the bond between the residues? pdb2gmx do that automatically for
> CYS-CYS, right? but not for my new residue.
> 

This behavior is a product of specbond.dat, which is step #6 in the link I 
posted above.  You'll have to create your own entry in this file to achieve this 
function.

-Justin

> /EE
> 
> 
> 

-- 
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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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