[gmx-users] joining proteins at terminals

[Kit Sang Chu]

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.

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
>> >
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>
>