[gmx-users] joining proteins at terminals

[paul buscemi]

thanks for the note. Yes I meant a single chain name.  
The minimization for those few bonds should not be too arduous.  Hope it works out.
Paul

> On Oct 10, 2018, at 1:22 PM, Kit Sang Chu <kschu at ucdavis.edu> wrote:
> 
> Hi Paul,
> 
> Giving the same name you mean same "chain name"? I tried but the problem
> persists. For my specific case I cannot add extra amino acids. I just have
> to minimize the energy to pull them closer.
> 
> Regards,
> Simon Kit Sang Chu
> Ph.D. student
> Biophysics Graduate Group
> University of California Davis
> 
> 
> On Wed, Oct 10, 2018 at 3:48 AM paul buscemi <pbuscemi at q.com> wrote:
> 
>> Try giving residues in the macro-macro structure the same name … or
>> possibly get rid of the 10A gap by using additional amino acids like
>> gly-gly gly ?
>> 
>> 
>>> On Oct 9, 2018, at 5:28 PM, Kit Sang Chu <kschu at ucdavis.edu> wrote:
>>> 
>>> Hi everyone,
>>> 
>>> I have a macromolecular structure which contains multiple copies of
>>> proteins. Initially, there are separate monomers and now I have to join
>>> some of them through N/C-terminals.
>>> 
>>> However, editconf fails to recognize the merging part, possibly because
>>> they are separated by ~ 10A. All monomers supposed to be merged are given
>>> the same chain name in pdb. All hydrogen and terminal oxygens are
>> stripped
>>> out.
>>> 
>>> Are there any criteria specifically for GROMACS to recognize for merging?
>>> Is there any specification / flag to force merging terminals?
>>> 
>>> Thanks,
>>> Simon
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