[gmx-users] constraint and restraints

[Tsjerk Wassenaar]

Hi Niyaz,

In pymol you can try this (assuming your proteins are called proteinA and
proteinB):

import numpy
d = numpy.array(cmd.get_model("proteinA").get_coord_list())
d -= numpy.array(cmd.get_model("proteinB").get_coord_list())
d = (d**2).sum(axis=1).tolist()
tmp = list(d)
alter proteinA, b=tmp.pop(0)
alter proteinB, b=d.pop(0)
spectrum b, rainbow, proteinA or proteinB

Note this doesn't give the per-residue RMSD, but does the per-atom RMSD.
The per-residue RMSD is a bit odd, as it doesn't tell you all about the
backbone and doesn't tell you about the side chain. If you want the
backbone-per-residue, choosing C-alphas should be good enough. For the side
chains, you might want to consider dihedral angle RMSDs in stead.

Hope it helps,

Tsjerk


On Mon, Oct 6, 2014 at 1:55 PM, niyaz.sabir <niyaz.sabir at gmail.com> wrote:

>  Dear Tsjerk,
>
> Thank you very much. You are always ready to help.
>
> I have understood and taken your note : "Whether it makes sense is another
> question. The dynamics is usually coupled throughout the protein."
>
> With very best regards,
>
> Niyaz
>
> ----- Original Message -----
> *From:* Tsjerk Wassenaar <tsjerkw at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org> ;
> niyaz.sabir <niyaz.sabir at gmail.com>
> *Sent:* Monday, October 06, 2014 1:13 AM
> *Subject:* Re: [gmx-users] constraint and restraints
>
> Hi Niyaz,
>
> You can set position restraints for all atoms not in that residue range.
> Whether it makes sense is another question. The dynamics is usually coupled
> throughout the protein.
>
> Cheers,
>
> Tsjerk
>
> On Sun, Oct 5, 2014 at 10:03 PM, niyaz.sabir <niyaz.sabir at gmail.com>
> wrote:
>
>> Dear GROMACS  users,
>> Is it possible with Gromacs and how could be done a simulation keeping
>> almost all  protein residues fixed except for instance resi 361-372 ? Will
>> the extraction of resulting rmsd for each residue give some knowledge
>> regarding its flexibility (mobility) ?
>> Regards, N.S.
>> --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.