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

Justin A. Lemkul jalemkul at
Wed Jan 12 17:08:55 CET 2011

Edvin Erdtman wrote:
>> "Justin A. Lemkul" wrote: Please see the following: 
> 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 


> /EE


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080


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