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.abra...@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@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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