Re: [gmx-users] Protein-ligand binding Cut-offs

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 there are

Re: [gmx-users] Protein-ligand binding Cut-offs

maillist.sys.kth.se [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

Re: [gmx-users] Protein-ligand binding Cut-offs

] 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, 2017 at 12:16

Re: [gmx-users] Protein-ligand binding Cut-offs

; 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: 28 June 2017 11:08 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-

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 <akash.pandya...@ucl.ac.uk> wrote: > Hi, > > I want to select all the ligands in my box within 4A of my protein. I > looked at gmx

Re: [gmx-users] Protein-ligand binding Cut-offs

ot; and within 0.4 of com of 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 Jun

Re: [gmx-users] Protein-ligand binding Cut-offs

s-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" and its suggestions fo

Re: [gmx-users] Protein-ligand binding Cut-offs

_mol_com > -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: gm

Re: [gmx-users] Protein-ligand binding Cut-offs

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 binding Cut

Re: [gmx-users] Protein-ligand binding Cut-offs

rom: "Mark Abraham" <mark.j.abra...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> 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

Re: [gmx-users] Protein-ligand binding Cut-offs

gt; > -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 bind

Re: [gmx-users] Protein-ligand binding Cut-offs

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 <akash.pandya...@ucl.ac.uk> wrote:

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 have ran a simulation with a protein and multiple ligand molecules >

[gmx-users] Protein-ligand binding Cut-offs

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