[gmx-users] joining proteins at terminals

[Justin Lemkul]

On 10/10/18 5:57 PM, Kit Sang Chu wrote:
> Hi everyone,
>
> In general, what is the GROMACS's criteria to bond terminals? I should
> check whether I have met all of them. Perhaps I miss one or two.

I don't follow what you're trying to do. editconf doesn't make bonds. 
pdb2gmx does, but it only links what you tell it. You can tell pdb2gmx 
to bond anything at any distance with an .rtp entry, but you'll get a 
long bond warning and your system may not minimize if the C-N distance 
is indeed 10 A.

-Justin

> Regards,
> Simon Kit Sang Chu
> Ph.D. student
> Biophysics Graduate Group
> University of California Davis
>
>
> On Wed, Oct 10, 2018 at 11:22 AM 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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