in Lemkul
wrote:
>
> Subject:
Re: [gmx-users] RMSD plots protein-peptide complex
> To: gmx-us...@gromacs.org
> Date: Thursday, 10 January, 2019, 4:19
PM
>
>
>
> On 1/10/19
6:31 AM, Dr. Seema Mishra wrote:
>
>
> > Thanks Justin.
&g
), then create an index group with just those atoms so you can
use it for analysis.
-Justin
On Thu, 10/1/19, Justin Lemkul wrote:
Subject: Re: [gmx-users] RMSD plots protein-peptide complex
To: gmx-us...@gromacs.org
Date: Thursday, 10 January
. Otherwise, How to get
that?
On Thu, 10/1/19, Justin Lemkul wrote:
Subject: Re: [gmx-users] RMSD plots protein-peptide complex
To: gmx-us...@gromacs.org
Date: Thursday, 10 January, 2019, 4:19 PM
On 1/10/19 6:31 AM, Dr. Seema Mishra wrote
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
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
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
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.
Thanks in anticipation
--
