Select interface residues with gmx select tool

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Dear all,

My problem consist in to select the alpha-carbons of protein-protein interface using gmx select tool, aim to calculate the evolution of RMSD over time from a molecular dynamics trajectory. However, I’ve found trouble with how to do it. I tried a couple of commands based on VMD syntax but doesn’t work in any scenarios. For example, the VMD command below makes the right selection in VMD, but similar syntaxes doesn’t work on gmx select.

“name CA and ((same residue as within 0.4 of protein1) and (same residue as within 0.4 of protein2))”

Any comments/tips are welcome. Thanks in advance!

Best,
-CC

2

Hi,
you can use

gmx help selections

to get help on the selection syntax or

http://manual.gromacs.org/documentation/current/onlinehelp/selections.html?highlight=selection%20syntax

Best regards
Alessandra

3

Dear Alessandra,

Thanks for replay. I already found the solution through the such informations. Following below the right command as a contribution for Gromacs community.

gmx select -f .gro -s .tpr -n Protein.ndx -on Interface.ndx -select “name CA and ((group Protein1 and within 0.4 of group Protein2) or (group Protein2 and within 0.4 of group Protein1))”

It works for selection of CA atoms at the interface from both proteins.

Best,
-CC