[gmx-users] RMSD plots protein-peptide complex
Dr. Seema Mishra
seema_uoh at yahoo.com
Fri Jan 11 04:28:53 CET 2019
Ok I understand. We create index groups for backbone atoms of selected protein only. I made index group for whole residues of selected protein. Will do again. Ok then let us see.
--------------------------------------------
On Fri, 11/1/19, Justin Lemkul <jalemkul at vt.edu> wrote:
Subject: Re: [gmx-users] RMSD plots protein-peptide complex
To: gmx-users at gromacs.org
Date: Friday, 11 January, 2019, 1:56 AM
On 1/10/19 8:23 PM, Dr. Seema Mishra wrote:
> Ok so I created index group already and
fed it ti trjconv and g_rms. But while selecting atoms in
g_rms stage if we select 22 (for index group) then all atoms
of index group will be selected. We want inly backbone atoms
of index group. I thought my commands just written before
here would work. Otherwise, How to get that?
Like I said before, you need
to create an index group that has the atoms
you want to analyze. I don't know what
group 22 is and you're not
posting
complete information. If you want the backbone of the
protein
(receptor), then create an index
group with just those atoms so you can
use
it for analysis.
-Justin
>
--------------------------------------------
> On Thu, 10/1/19, Justin Lemkul <jalemkul at vt.edu>
wrote:
>
> Subject:
Re: [gmx-users] RMSD plots protein-peptide complex
> To: gmx-users at gromacs.org
> Date: Thursday, 10 January, 2019, 4:19
PM
>
>
>
> On 1/10/19
6:31 AM, Dr. Seema Mishra wrote:
>
>
> > Thanks Justin.
> > Are these two commands for RMSD OK
after
> making index groups for
protein only? Forgive my
>
silliness:
> > gmx trjconv -s
md_0_1.tpr -f
> md_0_1.xtc -n
index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur
> compact
> >
Select 0
> >
>
> gmx rms -s md_0_1.tpr
> -f
md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns
> >
> >
Select 4 4 for
> backbone atoms. I
think then GROMACS will recognize only the
> index groups will be used for
identifying backbones
> >
>
> Sure,
> GROMACS does what you tell it. If you
choose the default
> group 4
> (Backbone), it will consider all
> atoms that qualify as backbone,
> encompassing any protein in the system.
What
> you need to do is create an
> index group
>
with only the relevant atoms of the protein receptor (not
>
> the peptide
ligand) and use that group for
>
analysis. The mere presence
> of a
> protein-only index group will do
nothing for you; you need
> to
> actually use it.
>
> -Justin
>
> >
> >
On Wednesday, 9
> January, 2019,
8:30:52 PM IST, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >
> >
> >
> > On 1/9/19 6:07 AM,
> Dr. Seema Mishra wrote:
> >> Hello
>
>> Any idea how to generate RMSD plots
> for only the protein in a
protein-peptide complex? I mean,
> do
give me commands for using only the protein backbone
> atoms as the g_rmsd uses all backbone
atoms of peptide as
> well and I do
not want peptide RMSD plots included.
>
> Make an index group that includes only the
> atoms you want to analyze.
> >
> >
-Justin
> >
>
> --
>
==================================================
>
> Justin A.
Lemkul, Ph.D.
> Assistant Professor
> Office: 301
>
Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech
Department of
> Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu
> | (540) 231-3129
>
http://www.thelemkullab.com
>
>
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301
Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of
Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu
| (540) 231-3129
http://www.thelemkullab.com
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