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

[Mark Abraham]

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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