[gmx-users] joining proteins at terminals

[Justin Lemkul]

On 10/11/18 2:21 AM, Kit Sang Chu wrote:
> Thanks, Justin. For the current state, it is still exploratory so I will
> try to avoid adding extra residues as linkers. Yes, I meant pdb2gmx. Sorry
> for the confusion.
>
> You mention I can feed in a .rtp file as an entry. How should I do that
> specifically?

There's nothing really to do. You concatenate the coordinates of the 
proteins, give them the same chain identifier (or ensure there are no 
TER cards between them) and run pdb2gmx. It should process it as a 
single protein.

-Justin

> Regards,
> Simon Kit Sang Chu
> Ph.D. student
> Biophysics Graduate Group
> University of California Davis
>
>
> On Wed, Oct 10, 2018 at 2:59 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>>> --
>>>>>> Gromacs Users mailing list
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================