lf Of Mark
Abraham
Sent: 28 June 2017 15:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
Hi,
You get to choose... do you want everything within some distance of the protein
center of mass, or any protein atom, or something else. But don't be suprrised
if ther
mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 28 June 2017 11:34
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> How are you interpreting "within 4A of my protein?" What has your
>
sys.kth.se] On Behalf Of Mark
Abraham
Sent: 28 June 2017 11:34
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
How are you interpreting "within 4A of my protein?" What has your protein's
center of mass got to do with it?
Mark
On Wed, Jun 28
--Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 28 June 2017 11:08
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
: Re: [gmx-users] Protein-ligand binding Cut-offs
Is the radius of your protein greater than 0.4 nm?
Mark
On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote:
> Hi,
>
> I want to select all the ligands in my box within 4A of my protein. I
> looked at gmx help select and I used the comma
f group "1"'
>
> Many thanks,
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 21 June 2017 11:56
> To: gmx-u
mx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 21 June 2017 11:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
Hi,
You aren't getting output because you aren't actually making a selection - see
"gmx help select" an
gt; -seltype dyn_mol_com -pdbatoms all
>
> Akash
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 16 June 2017 17:22
> To: gmx-us...@gr
-seltype dyn_mol_com -pdbatoms all
Akash
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 16 June 2017 17:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand b
rom: "Mark Abraham"
To: "gmx-users"
Sent: Tuesday, June 20, 2017 8:40:33 PM
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
Hi,
No, that's not a prerequisite, but it is one approach.
Mark
On Tue, Jun 20, 2017 at 8:16 PM Pandya, Akash
wrote:
> H
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 16 June 2017 17:22
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> Hi,
>
&
17:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
Hi,
Gmx select will produce a selection eg of all molecules with an atom within a
cutoff of any atom in another molecule.
Mark
On Fri, 16 Jun 2017 18:15 Pandya, Akash wrote:
> Hi all,
>
> I h
Hi,
Gmx select will produce a selection eg of all molecules with an atom within
a cutoff of any atom in another molecule.
Mark
On Fri, 16 Jun 2017 18:15 Pandya, Akash wrote:
> Hi all,
>
> I have ran a simulation with a protein and multiple ligand molecules
> inserted randomly inside a box. I w
Hi all,
I have ran a simulation with a protein and multiple ligand molecules inserted
randomly inside a box. I want to isolate those ligand molecules that are
closest to the protein by a cut-off of four angstroms or so. Is there a command
I could use to do this for me or would I have to use a m
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