[gmx-users] Question: how fix protein without loops

[Ann Vakhrusheva]

I have complex of protein with DNA. The loops of this protein weren't determined, so I've built them. Now I want to minimize system with fixed protein and flexible loops, because there could be clashes. How can I do it?
Thank you for response. 

15.07.2016, 22:46, "Mark Abraham" <mark.j.abraham at gmail.com>:
> Hi,
>
> I'm not sure what you're trying to do, or why loops are a concern. Are you
> trying to generate position restraints for multiple molecules when
> assembled together?
>
> Mark
>
> On Fri, Jul 15, 2016 at 2:18 PM Ann Vakhrusheva <vakhrusheva.ann at yandex.ru>
> wrote:
>
>>  Hello!
>>  I would like to restrain my protein but without loops before minimization.
>>  Can anyone advise me something?
>>  I was trying to make ndx file. As I understand, in this format all
>>  residues starts from 1 and don't split into chains by numbers (I mean, for
>>  example, a chain B doesn't start from 1, but continues a chain A). My
>>  protein has 2 chains (+2 chains of DNA), so when I want to exclude loops in
>>  chain B, I get restraints starts not from beginning of chain B, but
>>  subsequent restraints starting in chain A.
>>  So I have the error, that my chain B doesn't correspond to the molecule
>>  and I have to move it to the right molecule (in my file
>>  'topol_Protein_chain_B.itp' the chain B starts from 1 as separate chain).
>>  Maybe I can change numbering in list of residues during make_ndx? Or maybe
>>  here's another way?
>>  Thank you for any help.
>>  --
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